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object name.

output file from Cell Ranger used for creation of Seurat object.(Either provide this ofhdf5_file)

output file from Cell Ranger used for creation of Seurat object.(Either provide this offeatures_tsv_file)

name of assay(s) to add the alternative features to. Can specify "all"to add to all assays.

name to use for data.frame when stored in⁠@misc⁠ slot.

logical, whether to overwrite item with the samedata_name in the⁠@misc⁠ slot of object (default is FALSE).

object name.

name of the assay containing the raw data.

name of the assay containing the Cell Bender'ed data.

Seurat or LIGER object

Arguments passed to other methods

name to use for new meta data column. Default is "log10GenesPerUMI".

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning thatfunction will abort if column with name provided tometa_col_name is present in meta.data slot.

assay to use in calculation. Default is "RNA".Note This should only be changed ifstoring corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

Seurat or LIGER object

Arguments passed to other methods

logical, whether to add percentage of counts belonging to mitochondrial/ribosomalgenes to object (Default is TRUE).

logical, whether to add Cell Complexity to object (Default is TRUE).

logical, whether to add Top Gene Percentages to object (Default is TRUE).

logical, whether to add percentages of counts belonging to genes from of mSigDB hallmarkgene lists: "HALLMARK_OXIDATIVE_PHOSPHORYLATION", "HALLMARK_APOPTOSIS", and "HALLMARK_DNA_REPAIR" toobject (Default is TRUE).

logical, whether to add percentage of counts belonging to IEG genes to object (Default is TRUE).

logical, whether to add percentage of counts belonging to homoglobin genes to object (Default is TRUE).

logical, whether to add percentage of counts belonging to lncRNA genes to object (Default is TRUE).

logical, whether to addcell cycle scores and phase based onCellCycleScoring. Only applicable ifspecies = "human". (Default is TRUE).

Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat,drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automaticallygenerate patterns and features.

name to use for the new meta.data column containing percent mitochondrial counts.Default is "percent_mito".

name to use for the new meta.data column containing percent ribosomal counts.Default is "percent_ribo".

name to use for the new meta.data column containing percentmitochondrial+ribosomal counts. Default is "percent_mito_ribo".

name to use for new meta data column forAdd_Cell_Complexity.Default is "log10GenesPerUMI".

name to use for new meta data column forAdd_Top_Gene_Pct.Default is "percent_topXX", where XX is equal to the value provided tonum_top_genes.

name to use for new meta data column for percentage of MSigDB oxidative phosphorylationcounts. Default is "percent_oxphos".

name to use for new meta data column for percentage of MSigDB apoptosis counts.Default is "percent_apop".

name to use for new meta data column for percentage of MSigDB DNA repaircounts. Default is "percent_dna_repair"..

name to use for new meta data column for percentage of IEG counts. Default is "percent_ieg".

name to use for the new meta.data column containing percent hemoglobin counts.Default is "percent_mito".

name to use for the new meta.data column containing percent lncRNA counts.Default is "percent_lncRNA".

A regex pattern to match features against for mitochondrial genes (will set automatically ifspecies is mouse or human; marmoset features list saved separately).

A regex pattern to match features against for ribosomal genes(will set automatically if species is in default list).

A regex pattern to match features against for hemoglobin genes(will set automatically if species is in default list).

A list of mitochondrial gene names to be used instead of using regex pattern.Will override regex pattern if both are present (including default saved regex patterns).

A list of ribosomal gene names to be used instead of using regex pattern.Will override regex pattern if both are present (including default saved regex patterns).

A list of hemoglobin gene names to be used instead of using regex pattern.Will override regex pattern if both are present (including default saved regex patterns).

logical, whether feature names in the object are gene names orensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

An integer vector specifying the size(s) of the top set of high-abundance genes.Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.

assay to use in calculation. Default is "RNA".Note This should only be changed ifstoring corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

returns list of all accepted values to use for default species names whichcontain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, andchicken). Default is FALSE.

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning thatfunction will abort if column with name provided tometa_col_name is present in meta.data slot.

logical, whether to add module score belonging to IEG genes to object (Default is TRUE).

name to use for new meta data column for module score of IEGs. Default is "ieg_score".

Seurat or LIGER object

Arguments passed to other methods

Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat,drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automaticallygenerate hemo_pattern values.

name to use for the new meta.data column containing percent hemoglobin counts.Default is "percent_hemo".

A regex pattern to match features against for hemoglobin genes (will set automatically ifspecies is mouse or human; marmoset features list saved separately).

A list of hemoglobin gene names to be used instead of using regex pattern.

logical, whether feature names in the object are gene names orensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning thatfunction will abort if columns with any one of the names provided tohemo_name ispresent in meta.data slot.

returns list of all accepted values to use for default species names whichcontain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, andrhesus macaque). Default is FALSE.

Assay to use (default is the current object default assay).

Seurat or LIGER object

Arguments passed to other methods

Species of origin for given Seurat Object. Only accepted species are: mouse, human (name or abbreviation).

column name in meta.data that contains sample ID information.

name to use for the new meta.data column containing percent IEG gene counts.Default is set dependent on species gene symbol.

logical, whether feature names in the object are gene names orensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

Assay to use (default is the current object default assay).

Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning thatfunction will abort if columns with the name provided tomalat1_threshold_name is present in meta.data slot.

logical, should plots be printed to output when running function (default is NULL).Will automatically set to FALSE if performing across samples or TRUE if performing across whole object.

logical, whether or not to save plots to pdf (default is FALSE).

path to save location for plots (default is NULL; current working directory).

name for pdf file containing plots.

the width (in inches) for output page size. Default is 11.

the height (in inches) for output page size. Default is 8.

logical, whether to perform calculation on whole object (default is FALSE).Should be only be run if object contains single sample.

feature name for MALAT1 homolog in non-default species (if annotated).

The "bandwidth" value when plotting the density function to the MALAT1 distribution;default is bw = 0.1, but this parameter should be lowered (e.g. to 0.01) if you run the function andthe line that's produced doesn't look like it's tracing the shape of the histogram accurately (this willmake the line less "stiff" and more fitted to the data)

The "line width" fed to the abline function which adds the vertical red line to the output plots;default is 2, and it can be increased or decreased depending on the user's plotting preferences

The number of bins used for plotting the histogram of normalized MALAT1 values; default is 100

The minimum MALAT1 value cutoff above which a MALAT1 peak in the density function shouldbe found. This value is necessary to determine which peak in the density function fitted to the MALAT1distribution is likely representative of what we would expect to find in real cells. This is becausesome samples may have large numbers of cells or empty droplets with lower than expected normalized MALAT1 values,and therefore have a peak close to or at zero. Ideally, "chosen_min" would be manually chosen after looking ata histogram of MALAT1 values, and be the normalized MALAT1 value that cuts out all of the cells that look likethey stray from the expected distribution (a unimodal distribution above zero). The default value is 1 as thisworks well in many test cases, but different types of normalization may make the user want to change thisparameter (e.g. Seurat's original normalization function generates different results to their SCT function)which may change the MALAT1 distribution). Increase or decrease chosen_min depending on where your MALAT1 peak is located.

The "smoothing parameter" fed into the "smooth.spline" function that adjusts the trade-off betweenthe smoothness of the line fitting the histogram, and how closely it fits the histogram; the default is 1,and can be lowered if it looks like the line is underfitting the data, and raised in the case of overfitting.The ideal scenario is for the line to trace the histogram in a way where the only inflection point(s) are betweenmajor peaks, e.g. separating the group of poor-quality cells or empty droplets with lower normalized MALAT1expression from higher-quality cells with higher normalized MALAT1 expression.

The absolute lowest value allowed as the MALAT1 threshold. This parameter increases therobustness of the function if working with an outlier data distribution (e.g. an entire sample is poorquality so there is a unimodal MALAT1 distribution that is very low but above zero, but also manyvalues close to zero) and prevents a resulting MALAT1 threshold of zero. In the case where a calculatedMALAT1 value is zero, the function will return 0.3 by default.

A rough value for the location of a MALAT1 peak if a peak is not found. This is possibleif there are so few cells with higher MALAT1 values, that a distribution fitted to the data finds no local maxima.For example, if a sample only has poor-quality cells such that all have near-zero MALAT1 expression,the fitted function may look similar to a positive quadratic function which has no local maxima.In this case, the function searches for the closest MALAT1 value to the default value, 2, to use in place ofa real local maximum.

Seurat or LIGER object

Arguments passed to other methods

Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat,drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automaticallygenerate mito_pattern and ribo_pattern values.

name to use for the new meta.data column containing percent mitochondrial counts.Default is "percent_mito".

name to use for the new meta.data column containing percent ribosomal counts.Default is "percent_ribo".

name to use for the new meta.data column containing percentmitochondrial+ribosomal counts. Default is "percent_mito_ribo".

A regex pattern to match features against for mitochondrial genes (will set automatically ifspecies is mouse, human, zebrafish, rat, drosophila, rhesus macaque, or chicken;marmoset features list saved separately).

A regex pattern to match features against for ribosomal genes(will set automatically if species is mouse, human, marmoset, zebrafish, rat,drosophila, rhesus macaque, or chicken).

A list of mitochondrial gene names to be used instead of using regex pattern.Will override regex pattern if both are present (including default saved regex patterns).

A list of ribosomal gene names to be used instead of using regex pattern.Will override regex pattern if both are present (including default saved regex patterns).

logical, whether feature names in the object are gene names orensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning thatfunction will abort if columns with any one of the names provided tomito_nameribo_name ormito_ribo_name is present in meta.data slot.

returns list of all accepted values to use for default species names whichcontain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, andchicken). Default is FALSE.

Assay to use (default is the current object default assay).

the species prefix in front of gene symbols in object if providing two species formulti-species aligned dataset.

data.frame containing the results ofFindMarkers,FindAllMarkers, or other DE test data.frame.

the name of data.frame column corresponding to percent expressed in group 1.Default is Seurat default "pct.1".

the name of data.frame column corresponding to percent expressed in group 2.Default is Seurat default "pct.2".

logical. If themarker_dataframe already contains column named "pct_diff" whether tooverwrite or return error message. Default is FALSE.

object name.

data.frame/tibble containing meta data or path to file to read. Must be formatted aseither data.frame or tibble.

name of the column inseurat_object@meta.data that contains matchingvariables tojoin_by_meta inmeta_data.

name of the column inmeta_data that contains matchingvariables tojoin_by_seurat inseurat_object@meta.data.

logical, is it ok to add NA values toseurat_object@meta.data. Default is FALSE.Be very careful if setting TRUE because if there is error in join operation it may result in all⁠@meta.data⁠ values being replaced with NA.

logical, if there are shared columns betweenseurat_object@meta.data andmeta_datashould the currentseurat_object@meta.data columns be overwritten. Default is FALSE. This parameterexcludes values provided tojoin_by_seurat andjoin_by_meta.

Seurat or LIGER object.

Arguments passed to other methods

An integer vector specifying the size(s) of the top set of high-abundance genes.Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.

name to use for new meta data column. Default is "percent_topXX", where XX isequal to the value provided tonum_top_genes.

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning thatfunction will abort if column with name provided tometa_col_name is present in meta.data slot.

logical, whether to print messages with status updates, default is TRUE.

assay to use in calculation. Default is "RNA".Note This should only be changed ifstoring corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

DFrame output frombarcodeRanks.

point size for plotting, default is 6.

Title for plot, default is "Barcode Ranks".

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(1024, 1024).

numerical value at which to add vertical line designating estimatedempty droplet plateau (default is NULL).

extra arguments passed toggplot2::theme().

Seurat object name.

vector of genes to check.

logical. Whether to print message to console if alternate case features arefound in addition to inclusion in returned list. Default is TRUE.

logical. Whether to return vector of alternate case features. Default is TRUE.

Name of assay to pull feature names from. If NULL will use the result ofDefaultAssay(seurat_object).

name of data.frame created usingCellBender_Feature_Diff.

threshold to use for feature plotting. Resulting plot will only containfeatures which exhibit percent change >= value. Default is 25.

Number of features to plot. Will ignorepct_diff_threshold and returnplot with specified number of features. Default is NULL.

logical, whether or not to label the features that have largest percent differencebetween raw and CellBender counts (Default is TRUE).

Number of features to label iflabel = TRUE, (default is 20).

Minimum number of raw counts per feature necessary to be included inplot labels (default is 1)

logical, whether to use geom_text_repel to create a nicely-repelled labels; this isslow when a lot of points are being plotted. If using repel, set xnudge and ynudge to 0, (Default is TRUE).

A custom set of features to label instead of the features most different betweenraw and CellBender counts.

logical, whether to plot diagonal line with slope = 1 (Default is TRUE).

Plot title.

Label for x axis.

Label for y axis.

Amount to nudge X and Y coordinates of labels by.

Amount to nudge X and Y coordinates of labels by.

passed togeom_text_repel, exclude text labels thatoverlap too many things. Defaults to 100.

Color to use for text labels.

font face to use for text labels (“plain”, “bold”, “italic”, “bold.italic”) (Default is "bold").

text size for feature labels (passed togeom_text_repel).

color to use for shadow/outline of text labels (passed togeom_text_repel) (Default is white).

radius to use for shadow/outline of text labels (passed togeom_text_repel) (Default is 0.15).

Extra parameters passed togeom_text_repel throughLabelPoints.

Seurat object name.

Name of the assay containing the raw count data.

Name of the assay containing the CellBender count data.

Name of raw count matrix in environment if not using Seurat object.

Name of CellBender count matrix in environment if not using Seurat object.

Seurat object name.

Cell names to highlight in named list.

Color to highlight cells.

non-highlighted cell colors (default is "lightgray")..

point size for both highlighted cluster and background.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denotingaxes labels. (Default is FALSE). Requiressplit_seurat = TRUE.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Whether to label the highlighted meta data variable(s). Default is FALSE.

Variable in⁠@meta.data⁠ to split the plot by.

logical. Whether or not to display split plots like Seurat (shared y axis) or asindividual plots in layout. Default is FALSE.

Dimensionality Reduction to use (if NULL then defaults to Object default).

logical. Ifhighlight_color = NULL, Whether or not to return plotusing default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Extra parameters passed toDimPlot.

LIGER object name.

logical, whether to return list with vector of cell barcodes for eachdataset in LIGER object or to return single vector of cell barcodes across alldatasets in object (default is FALSE; return vector of cells).

Arguments passed to other methods

LIGER object name.

name of meta data column to use, default is current default clustering.

logical, whether to return list with entries for cell barcodes for eachidentity ingroup.byor to return list of lists (1 entry per dataset and each ident within the dataset)(default is FALSE; return list)

Seurat object

column name in meta.data that contains sample ID information. Default is NULL andwill use "orig.ident column

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value of current delimiter.

a single value of new delimiter desired.

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value of current delimiter.

a single value of new delimiter desired.

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value of current delimiter.

a single value of new delimiter desired.

A matrix

Type of checks to perform, choose one or more from:

• “infinite”: Emit a warning if any value is infinite

• “logical”: Emit a warning if any value is a logical

• “integer”: Emit a warning if any value isnotan integer

• “na”: Emit a warning if any value is anNAorNaN

Seurat object name.

Name(s) (or number(s)) identity of cluster to be highlighted.

Color(s) to highlight cells. The default is NULL and plot will usescCustomize_Palette().

non-highlighted cell colors.

point size for both highlighted cluster and background.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denotingaxes labels. (Default is FALSE). Requiressplit_seurat = TRUE.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Whether to label the highlighted cluster(s). Default is FALSE.

Feature to split plots by (i.e. "orig.ident").

logical. Whether or not to display split plots like Seurat (shared y axis) or asindividual plots in layout. Default is FALSE.

size for plot title labels when usingsplit.by.

Number of columns in plot layout. Only valid ifsplit.by != NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Extra parameters passed toDimPlot.

Seurat object name.

meta data column to classify samples (default = "orig.ident").

logical, whether the data.frame should be ordered by frequency ofidentity (default; TRUE), or by cluster/fector order (FALSE).

Seurat object name.

Features to plot.

a subset offeatures to only label some of the plotted features.

Variable in⁠@meta.data⁠ to split the identities plotted by.

Color palette to use for plotting expression scale. Default isviridis::plasma(n = 20, direction = -1).

Minimum scaled average expression threshold (everything smaller will be set to this).Default is -2.

What scaled expression value to use for the middle of the providedcolors_use_exp.By default will be set to value in middle ofexp_color_min andexp_color_max.

Minimum scaled average expression threshold (everything smaller will be set to this).Default is 2.

Whether to plot average normalized expression orscaled average normalized expression. Only valid whensplit.by is provided.

Whether to print the quantiles of expression data in addition to plots.Default is FALSE. NOTE: These values will be altered by choices ofexp_color_min andexp_color_minif there are values below or above those cutoffs, respectively.

specify color palette to used for identity labels. By default ifnumber of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36will use "varibow" with shuffle = TRUE both fromDiscretePalette_scCustomize.

logical, whether to show colors for idents on the column/rows of the plot(default is TRUE).

logical, whether or not to show annotation name next to color bar. Default isTRUE.

How to rotate column labels. By default set toTRUE which rotates labels 45 degrees.If setFALSE rotation is set to 0 degrees. Users can also supply custom angle for text rotation.

if plot needs extra white space padding so no plot or labels are cutoff.The parameter accepts TRUE or numeric vector of length 4. If TRUE padding will be set toc(2, 10, 0 0) (bottom, left, top, right). Can also be customized further with numericvector of length 4 specifying the amount of padding in millimeters.Default is NULL, no padding.

logical, whether to flip the axes of final plot. Default is FALSE; rows = features andcolumns = idents.

Value to use for k-means clustering on features Sets (km) parameter inComplexHeatmap::Heatmap().FromComplexHeatmap::Heatmap(): Apply k-means clustering on rows. If the value is larger than 1, theheatmap will be split by rows according to the k-means clustering. For each row slice, hierarchicalclustering is still applied with parameters above.

Number of k-means runs to get a consensus k-means clustering for features.Note iffeature_km_repeats is set to value greater than one, the final number of groups might besmaller than row_km, but this might mean the original row_km is not a good choice. Default is 1000.

Number of k-means runs to get a consensus k-means clustering. Similar tofeature_km_repeats. Default is 1000.

Size of the feature labels. Provided torow_names_gp in Heatmap call.

Fontface to use for row labels. Provided torow_names_gp in Heatmap call.

color to use for heatmap grid. Default is NULL which "removes" grid by using NA color.

logical, whether to cluster and reorder feature axis. Default is TRUE.

logical, whether to cluster and reorder identity axis. Default is TRUE.

Size of the feature labels. Provided tocolumn_names_gp in Heatmap call.

Size of the legend text labels. Provided tolabels_gp in Heatmap legend call.

Size of the legend title text labels. Provided totitle_gp in Heatmap legend call.

Location of the plot legend (default is "right").

Orientation of the legend (default is NULL).

logical, whether to show the color legend for idents in plot (default is TRUE).

logical, whether to show row names on plot (default is TRUE).

logical, whether to show column names on plot (default is TRUE).

Should the row names be on the "bottom" or "top" of plot. Default is "bottom".

Should the row names be on the "left" or "right" of plot. Default is "right".

Logical, whether to render in raster format (faster plotting, smaller files). Default is FALSE.

Logical, whether or not to return the Sum Squared Error Elbow Plot for k-means clustering.Estimating elbow of this plot is one way to determine "optimal" value fork.Based on:https://stackoverflow.com/a/15376462/15568251.

The maximum value of k to use forplot_km_elbow. Suggest setting larger value so thetrue shape of plot can be observed. Value must be 1 less than number of features provided. If NULL parameterwill be set dependent on length of feature list up toelbow_kmax = 20.

Name of assay to use, defaults to the active assay.

Group (color) cells in different ways (for example, orig.ident).

Which classes to include in the plot (default is all).

Logical, Sets parameter of same name inComplexHeatmap::Heatmap().FromComplexHeatmap::Heatmap(): When heatmap is split, whether to add a dashed line to mark parentdendrogram and children dendrograms. Default is TRUE.

logical, default is FALSE.ONLY set this value to true if you get error related toNaN values when attempting to use plotting function. Plotting may be slightly slower if TRUE depending onnumber of features being plotted.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Sets seed for reproducible plotting (ComplexHeatmap plot).

Seurat object name.

name(s) of assays to convert. Default is NULL and will check with userswhich assays they want to convert.

value of what assay type to convert current assays to.#'

• Accepted values for V3/4 are: "Assay", "assay", "V3", or "v3".

• Accepted values for V5 are: "Assay5", "assay5", "V5", or "v5".

folder to be copied to GCP bucket.

GCP bucket path to copy to files.

folder to be copied to GCP bucket.

GCP bucket path to copy to files.

file path to raw data file(s).

type of source data (Default is "10X"). Alternatively can provide "Matrix" or "data.frame".

file path to directory to save file.

name prefix for output H5 file.

matrix file containing the cell bender correct counts.

matrix file contain the uncorrected Cell Ranger (or other) counts.

a key value to use specifying the name of assay. Default is "RAW".

value to supply to min.cells parameter ofCreateSeuratObject.Default is 5.

value to supply to min.features parameter ofCreateSeuratObject.Default is 200.

Extra parameters passed toCreateSeuratObject.

path to directory to save file. Default is current working directory.

name to use for annotation file. Function automatically adds file type ".csv" suffix.Default is "cluster_annotation".

LIGER object name.

other meta data to include in returned data.frame.

meta data column to filter data by. Will filter data to return only values for thelargest dataset for each unique value in provided meta data column.

logical, whether to print filtered results to console, default is FALSE.

Seurat object name.

Meta data column to split plots by.

single color to use for all plots or a vector of colors equal to the number of plots.

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

size for plot title labels.

number of columns in final layout plot.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Which dimensions to plot. Defaults to c(1,2) if not specified.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Extra parameters passed toDimPlot.

liger liger_object. Need to perform clustering before calling this function

Variable to be plotted. IfNULL will plot clusters fromliger@clusters slot.Ifcombination = TRUE will plot both clusters and meta data variable.Ifcombination = TRUE will plot both clusters and meta data variable.

Variable to split plots by.

colors to use for plotting by clusters. By default if number of levels plotted isless than or equal to 36 will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUEboth fromDiscretePalette_scCustomize.

colors to use for plotting by meta data (cell.data) variable. By default if numberof levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use"varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

Adjust point size for plotting.

logical. Whether to randomly shuffle the order of points. This can be useful for crowded plotsif points of interest are being buried. (Default is TRUE).

Sets the seed if randomly shuffling the order of points.

What to label the x and y axes of resulting plots. LIGER does not store name oftechnique and therefore needs to be set manually. Default is "UMAP". (only valid forrliger < 2.0.0).

specify reduction to use when plotting. Default is current objectdefault reduction (only valid for rliger v2.0.0 or greater).

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

logical. Whether or not to label the clusters. ONLY applies to plotting by cluster. Default is TRUE.

size of cluster labels.

logical. Whether to repel cluster labels from each other if plotting bycluster (ifgroup.by = NULL or⁠group.by = "cluster⁠). Default is FALSE.

logical. Whether to put a box around the label text (usesgeom_text vsgeom_label).Default is FALSE.

Color to use for cluster labels. Default is "black".

logical, whether to return patchwork displaying both plots side by side. (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Number of columns in plot layout. Only valid ifsplit.by != NULL.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

color palette to use for plotting. By default if number of levels plotted is less thanor equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUEboth fromDiscretePalette_scCustomize.

Adjust point size for plotting.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Feature to split plots by (i.e. "orig.ident").

logical, whether to downsample the split plots by number of cells in the smallest group.Default is FALSE.

logical. Whether or not to display split plots like Seurat (shared y axis) or asindividual plots in layout. Default is FALSE.

logical. Whether to remove the axes and plot with legend on left of plot denotingaxes labels. (Default is FALSE). Requiressplit_seurat = TRUE.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

logical, whether to add plot to returned layout with the number of cells per identity(or percent of cells per identity). Default is FALSE.

logical, ifadd_prop_plot = TRUE this parameter controls whetherproportion plot shows raw cell number or percent of cells per identity. Default is FALSE; plots raw cell number.

logical, ifadd_prop_plot = TRUE this parameter controls whether to change x axisto log10 scale (Default is FALSE).

logical, ifadd_prop_plot = TRUE this parameter controls whether to label the bars with total number of cells or percentages; Default is FALSE.

logical. Whether to randomly shuffle the order of points. This can be useful for crowdedplots if points of interest are being buried. (Default is TRUE).

Sets the seed if randomly shuffling the order of points.

Whether to label the clusters. By default ifgroup.by = NULL label = TRUE, andotherwise it is FALSE.

Sets size of labels.

Sets the color of the label text.

Whether to put a box around the label text (geom_text vs geom_label).

Which dimensions to plot. Defaults to c(1,2) if not specified.

Repel labels.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Number of columns in plot layout. Only valid ifsplit.by != NULL.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed to use when selecting random cells to downsample in plot.Default = 123.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toDimPlot.

Number of colors to be generated.

Options are"alphabet", "alphabet2", "glasbey", "polychrome", "stepped", "ditto_seq", "varibow".

randomly shuffle the outputted palette. Most useful forvaribow palette asthat is normally an ordered palette.

random seed for the palette shuffle. Default = 123.

Seurat object name.

Features to plot.

Name of metadata variable (column) to group cells by (for example, orig.ident);default is the current active.ident of the object.

specify color palette to used. Default is viridis_plasma_dark_high.

logical. Whether to remove the x and y axis titles. Default = TRUE.

Rotate x-axis labels 45 degrees (Default is FALSE).

Rotate x-axis labels 45 degrees (Default is FALSE).

Rotate facet labels on groupedDotPlots by 45 degrees (Default is FALSE).

whether or not to flip and X and Y axes (Default is FALSE).

Extra parameters passed toDotPlot.

name of Seurat object

The number of dims to plot. Default is NULL and will plot all dims

The reduction to use, default is "pca"

logical, whether or not to calculate the cutoffs, default is TRUE.

lgoical, whether to plot the cutoffs as vertical lines on plot, default is TRUE.

colors for the cutoff lines, default is c("dodgerblue", "firebrick").

widith of the cutoff lines, default is 0.5.

LIGER object name.

name of dimensionality reduction to pull

logical, whether to extract iNMF h.norm matrix instead of dimensionality reduction embeddings.

logical, returnTRUE if valid reduction is present.

Arguments passed to other methods

list of matrices to split by modality

Seurat or LIGER object

meta.data column to use as sample. Output data.frame will contain one row perlevel or unique value in this variable.

. Seesample_name.

⁠@meta.data⁠ columns to keep in final data.frame. All other columns willbe discarded. Default is NULL.

columns to discard in final data.frame. Many cell level columns areirrelevant at the sample level (e.g., nFeature_RNA, percent_mito).

• Default parameter value isNULL but internally will set to discard nFeature_ASSAY(s),nCount_ASSAY(s), percent_mito, percent_ribo, percent_mito_ribo, and log10GenesPerUMI.

• If sample level median values are desired for these type of variables the output of thisfunction can be joined with output ofMedian_Stats.

• Set parameter toinclude_all = TRUE to prevent any columns from being excluded.

logical, whether or not to include all object meta data columns in output data.frame.Default is FALSE.

data.frame output fromFindAllMarkers or similar analysis.

number of features per group (e.g., cluster) to include in output list.

soft-deprecated. Seenum_features.

soft-deprecated. Seegroup.by.

column name ofmarker_dataframe to group data by. Default is "cluster" based onFindAllMarkers.

column name ofmarker_dataframe to rank data by when selectingnum_genes pergroup.by.Default is "avg_log2FC" based onFindAllMarkers.

column name ofmarker_dataframe that contains the gene IDs. Default is "gene"based onFindAllMarkers.

logical. Whether gene IDs are stored in rownames and should be moved tocolumn. Default is FALSE.

Logical, whether or not to return filtered data.frame of the originalmarkers_dataframe orto return a vector of gene IDs. Default is FALSE.

Logical, whether or not to name the vector of gene names that is returned by the function.IfTRUE will name the vector using the column provided togroup.by. Default is TRUE.

Logical, whether an unnamed vector should return only unique values. Default is FALSE.Not applicable whendata_frame = TRUE ornamed_vector = TRUE.

LIGER or Seurat object.

Seurat ONLY; name of dimensionality reduction containing NMF loadings.

Color palette to use for correlation values.Default isRColorBrewer::RdBu ifpositive_only = FALSE.Ifpositive_only = TRUE the default isviridis.Users can also supply vector of 3 colors (low, mid, high).

logical, whether to add correlation values to plot result.

threshold for adding correlation values iflabel = TRUE. Defaultis 0.5.

size of correlation labels

Plot title.

Controls plotting full matrix, or just the upper or lower triangles.Accepted values are: "full" (default), "upper", or "lower".

logical, whether to limit the plotted values to only positivecorrelations (negative values set to 0); default is FALSE.

logical, whether to rotate the axes labels on the x-axis. Default is TRUE.

logical, whether to cluster the plot usinghclust (default TRUE). If FALSEfactors are listed in numerical order.

logical, whether to add rectangles around the clustered areas on plot,default is FALSE. Usescutree to create groups.

number of rectangles to add to the plot, default NULL.Value is provided tok incutree.

color to use for rectangles, default MULL (will set color automatically).

Seurat object name.

Feature(s) to plot.

name of assay one. Default is "RAW" as featured inCreate_CellBender_Merged_Seurat

name of assay two Default is "RNA" as featured inCreate_CellBender_Merged_Seurat

list of colors or color palette to use.

optional, a second color palette to use for the second assay.

color to use for points below lower limit.

whether to move positive cells to the top (default = TRUE).

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Value to use as minimum expression cutoff. To set no cutoff set toNA.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Which layer to pull expression data from? Default is "data".

Number of columns in plot layout. If number of features > 1 thennum_columnsdictates the number of columns in overall layout (num_columns = 1 means stacked layout &num_columns = 2means adjacent layout).

new alpha level to apply to expressing cell color palette (colors_use). Must bevalue between 0-1.

new alpha level to apply to non-expressing cell color palette (na_color). Must bevalue between 0-1.

Extra parameters passed toFeaturePlot.

Seurat object name.

Feature(s) to plot.

list of colors or color palette to use.

color to use for points below lower limit.

whether to move positive cells to the top (default = TRUE).

Adjust point size for plotting.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Value to use as minimum expression cutoff. This will be lowest value plotted usepalette provided tocolors_use. Leave as default value to plot only positive non-zero values usingcolor scale and zero/negative values as NA. To plot all values using color palette set toNA.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Variable in⁠@meta.data⁠ to split the plot by.

logical, whether to collect the legends/guides when plotting withsplit.by.Default is TRUE if one value is provided tofeatures otherwise is set to FALSE.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denotingaxes labels. (Default is FALSE). Requiressplit_seurat = TRUE.

Number of columns in plot layout.

Which layer to pull expression data from? Default is "data".

new alpha level to apply to expressing cell color palette (colors_use). Must bevalue between 0-1.

new alpha level to apply to non-expressing cell color palette (na_color). Must bevalue between 0-1.

logical, whether to label the clusters. Default is FALSE.

logical, whether to place feature labels on secondary y-axis as opposed toabove legend key. Default is FALSE. When settinglabel_feature_yaxis = TRUE the number of columnsin plot output will automatically be set to the number of levels in⁠split.by'⁠.

Vector of minimum and maximum cutoff values for each feature,may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').

Combine plots into a singlepatchworked ggplot object.If FALSE, return a list of ggplot objects.

Extra parameters passed toFeaturePlot.

Seurat object name.

First feature to plot.

Second feature to plot.

Cells to include on the scatter plot.

color for the points on plot.

Adjust point size for plotting.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident).Default is active ident.

Feature to split plots by (i.e. "orig.ident").

logical. Whether or not to display split plots like Seurat (shared y axis) or asindividual plots in layout. Default is FALSE.

logical, whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. Default is TRUE.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

size for plot title labels. Does NOT apply ifsplit_seurat = TRUE.

Display correlation in plot subtitle (or title ifsplit_seurat = TRUE).

number of columns in final layout plot.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toFeatureScatter.

Name of input data. Currently only data of classes: Seurat, liger, data.frame,dgCMatrix, dgTMatrix, tibble are accepted. Gene_IDs must be present in rownames of the data.

vector of features to check.

logical. Whether or not to check if features are found if the case is changed from theinput list (Sentence case to Upper and vice versa). Default is TRUE.

logical. Whether to print message to console if alternate case features are foundin addition to inclusion in returned list. Default is TRUE.

logical. Whether message should be printed if all features are found. Default is TRUE.

logical. Whether to print message about features that are not found in current object.Default is TRUE.

logical. Whether list of found vs. bad features should still be returned if nofeatures are found. Default is FALSE.

Name of assay to pull feature names from ifdata is Seurat Object.Default is NULL which will check against features from all assays present.

LIGER object name.

logical, whether to return list with vector of features for each dataset inLIGER object or to return single vector of unique features across all datasets in object(default is FALSE; return vector of unique features)

Arguments passed to other methods

Object of class Seurat or liger.

optional, name(s) of columns to return. Default is NULL; returns all columns

Arguments passed to other methods

LIGER/Seurat object name.

reduction name to pull loadings for. Only valid if supplying a Seurat object.

LIGER object name.

meta data column to use for selecting largest dataset.

value from columnmeta_data_column to use for selecting largest dataset.

number of colors to return in palette.

LIGER object name.

Arguments passed to other methods

name of column in cellMeta slot to set as new default cluster/ident

path to parent directory (ifmulti_directory = TRUE) or directory containingall h5 files (ifmulti_directory = FALSE).

logical, whether or not all h5 files are in their own subdirectories or in asingle directory (default is TRUE; each in own subdirectory (e.g. output from Cell Ranger)).

Either the file name of h5 file (ifmulti_directory = TRUE) or the sharedsuffix (ifmulti_directory = FALSE)

logical, whether the outputs to be read are from Cell Rangermulti as opposedto Cell Rangercount (default is FALSE). Only valid ifmulti_directory = FALSE.

logical, should files be read in parallel (default is FALSE).

Number of cores to use in parallel ifparallel = TRUE.

file path to use for saving PDF output.

Name of PDF output file.

point size for plotting, default is 6.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(1024, 1024).

numerical values at which to add vertical line designating estimatedempty droplet plateau (default is NULL). Must be vector equal in length to number of samples.

Additional parameters passed toRead10X_h5_Multi_Directory orRead10X_h5_GEO.

Seurat object name.

Color to highlight cells (default "navy"). Can provide either single color to use forall clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.

non-highlighted cell colors.

point size for both highlighted cluster and background.

Dimensionality Reduction to use (if NULL then defaults to Object default).

directory file path and/or file name prefix. Defaults to current wd.

name suffix to append after sample name.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Extra parameters passed toDimPlot.

Seurat object name.

name of meta.data column containing sample names/ids (default is "orig.ident").

directory file path and/or file name prefix. Defaults to current wd.

name suffix to append after sample name.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

color scheme to use.

logical, whether or not to include plot legend, default is TRUE.

Value that should be used for plot title prefix ifno_legend = TRUE.If NULL the value ofmeta_data_column will be used. Default is NULL.

Dimensionality Reduction to use (default is object default).

Dimensions to plot.

Adjust point size for plotting.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Extra parameters passed toDimPlot.

Seurat object name.

vector of features to plot. If a named vector is provided then the names for each genewill be incorporated into plot title ifsingle_pdf = TRUE or into file name ifFALSE.

color scheme to use.

color for non-expressed cells.

Value to use as minimum expression cutoff. To set no cutoff set toNA.

Variable in⁠@meta.data⁠ to split the plot by.

whether to move positive cells to the top (default = TRUE).

logical. Whether to return plots to list instead of saving them to file(s). Default is FALSE.

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE).

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

numeric, number of features to plot on single page ifsingle_pdf = TRUE. Default is 1.

Number of columns in plot layout (only applicable ifsingle_pdf = TRUE ANDfeatures_per_page > 1).

logical, when plotting multiple features per page in single PDF whether to use landscape or portraitpage dimensions (default is TRUE).

dpi for image saving.

Adjust point size for plotting.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

new alpha level to apply to expressing cell color palette (colors_use). Must bevalue between 0-1.

new alpha level to apply to non-expressing cell color palette (na_color). Must bevalue between 0-1.

Extra parameters passed toFeaturePlot.

Seurat object name.

Name of the column inseurat_object@meta.data slot to pull value from for highlighting.

The order in which to plot each level withinmeta_data_column ifsingle_PDF is TRUE.

logical. Whether or not to sort and relevel the levels inmeta_data_column ifsingle_PDF is TRUE. Default is TRUE.

Color to highlight cells (default "navy"). Can provide either single color to use forall clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.

non-highlighted cell colors.

point size for both highlighted cluster and background.

logical, whether or not to remove plot legend and move to plot title. Default is FALSE.

Value that should be used for plot title prefix ifno_legend = TRUE.If NULL the value ofmeta_data_column will be used. Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

directory file path and/or file name prefix. Defaults to current wd.

name suffix to append after sample name.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Extra parameters passed toDimPlot.

Seurat object name.

number of PCs to plot (integer). Default is all dims present in PCA.

directory file path to save file.

prefix for file name (optional).

suffix for file name. Default is "PC_Loading_Plots".

Whether to return the plot list (Default is FALSE). Must assign to environmentto save plot list.

Seurat object name.

vector of genes to plot. If a named vector is provided then the names for each genewill be incorporated into plot title ifsingle_pdf = TRUE or into file name ifFALSE.

color scheme to use.

color for non-expressed cells.

Adjust point size for plotting.

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Dimensionality Reduction to use (if NULL then defaults to Object default)

Create a single plot? If FALSE, a list with ggplot objects is returned.

NULL. This function only supportsjoint = FALSE. Leave as NULL to generate plots. To iterate joint plots see function:Iterate_Plot_Density_Joint.

Extra parameters passed toplot_density.

Seurat object name.

a list of vectors of genes to plot jointly. Each entry in the list will be plottedfor the joint density. All entries in list must be greater than 2 features. If a named list is providedthen the names for each list entry will be incorporated into plot title ifsingle_pdf = TRUE orinto file name ifFALSE.

color scheme to use.

color for non-expressed cells.

Adjust point size for plotting.

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Dimensionality Reduction to use (if NULL then defaults to Object default)

Create a single plot? If FALSE, a list with ggplot objects is returned.

NULL. This function only supportsjoint = FALSE. Leave as NULL to generate plots. To iterate joint plots see function:Iterate_Plot_Density_Joint.

Extra parameters passed toplot_density.

Seurat object name.

vector of features to plot.

color palette to use for plotting. By default if number of levels plotted is less thanor equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUEboth fromDiscretePalette_scCustomize.

point size for plotting.

Name of one or more metadata columns to group (color) plot by (for example, orig.ident);default is the current active.ident of the object.

Feature to split plots by (i.e. "orig.ident").

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

dpi for image saving.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object name.

meta data column to classify samples (default = "orig.ident").

logical. Whether to include the default meta.data variables of: "nCount_RNA","nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI"in addition to variables supplied tomad_var.

Column(s) in⁠@meta.data⁠ to calculate medians for in addition to defaults.Must be ofclass() integer or numeric.

integer value to multiply the MAD in returned data.frame (default is 2).Often helpful when calculating a outlier range to base of of median + (X*MAD).

name of Seurat object

current column in meta.data to map from

name of new column in meta.data to add new mapped variable. If NULL (default)will return the variable. If name provided will return Seurat object with new variable added.

Mapping criteria, argument names are original existing categoriesin thefrom calumn and values are new categories in the new variable.

Seurat object name.

meta data column to classify samples (default = "orig.ident").

logical. Whether to include the default meta.data variables of: "nCount_RNA","nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI"in addition to variables supplied tomedian_var.

Column(s) in⁠@meta.data⁠ to calculate medians for in addition to defaults.Must be ofclass() integer or numeric.

list composed of multiple Seurat Objects.

A character vector of equal length to the number of objects inlist_seurat.Appends the corresponding values to the start of each objects' cell names. Seemerge.

Merge the data slots instead of just merging the counts (which requires renormalization).This is recommended if the same normalization approach was applied to all objects.Seemerge.

Project name for the Seurat object. Seemerge.

list of matrices to merge.

a vector of sample ids to add as prefix to cell barcode during merge.

logical. Whetheradd_cell_ids should be added as prefix to current cell barcodes/namesor as suffix to current cell barcodes/names. Default is TRUE, add as prefix.

The delimiter to use when adding cell id prefix/suffix. Default is "_".

list of matrices to merge.

a vector of sample ids to add as prefix to cell barcode during merge.

logical. Whetheradd_cell_ids should be added as prefix to current cell barcodes/namesor as suffix to current cell barcodes/names. Default is TRUE, add as prefix.

The delimiter to use when adding cell id prefix/suffix. Default is "_".

Seurat object name.

Name of the column inseurat_object@meta.data slot to pull value from for highlighting.

Name of variable(s) withinmeta_data_name to highlight in the plot.

Color to highlight cells (default "navy").

non-highlighted cell colors.

point size for both highlighted cluster and background.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denotingaxes labels. (Default is FALSE). Requiressplit_seurat = TRUE.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Whether to label the highlighted meta data variable(s). Default is FALSE.

Variable in⁠@meta.data⁠ to split the plot by.

logical. Whether or not to display split plots like Seurat (shared y axis) or asindividual plots in layout. Default is FALSE.

Dimensionality Reduction to use (if NULL then defaults to Object default).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Extra parameters passed toDimPlot.

a data.frame contain meta.data.

Seurat or Liger object name.

vector of column names to check.

logical. Whether message should be printed if all features are found. Default is TRUE.

logical. Whether to print message about features that are not found in current object. Default is TRUE.

logical. Whether list of found vs. bad features should still be returned if nometa_col_names are found. Default is FALSE.

data.frame containing meta data.

object name.

logical, are barcodes present as column and should they be moved torownames (to be compatible withSeurat::AddMetaData). Default is FALSE.

name of barcodes column in meta_data. Required ifbarcodes_to_rownames = TRUE.

valid position to move legend. Default is "right".

extra arguments passed toggplot2::theme().

logical, whether to flip the order of colors.

Seurat Object.

A single dim to plot (integer).

a vector of colors (either named colors of hex codes).

logical, whether or not to numerically label the colors in output plot.Default is TRUE is number of colors inpal is less than 75 and FALSE is greater than 75.

Seurat object name.

Feature(s) to plot.

Expression threshold to use for calculation of percent expressing (default is 0).

Factor to group the cells by.

Factor to split the groups by.

logical (default = FALSE). Whether to calculate percent of expressing cellsacross the entire object as opposed to by cluster or bygroup.by variable.

Which layer to pull expression data from? Default is "data".

Assay to pull feature data from. Default is active assay.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use.

size of the dots plotted ifgroup.by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

Features to plot.

logical. Whether to return joint density plot. Default is FALSE.

default viridis palette to use (must be one of: "viridis", "magma", "cividis","inferno", "plasma"). Default is "magma".

non-default color palette to be used in place of default viridis options.

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Create a single plot? If FALSE, a list with ggplot objects is returned.

Extra parameters passed toplot_density.

Seurat object name.

Features to plot.

default viridis palette to use (must be one of: "viridis", "magma", "cividis","inferno", "plasma"). Default is "magma".

non-default color palette to be used in place of default viridis options.

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value;Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Extra parameters passed toplot_density.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable ifgroup.by is not NULL.

size of the dots plotted ifgroup.by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable ifgroup.by is not NULL.

size of the dots plotted ifgroup.by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

Variable in meta.data slot to calculate and plot median values for.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable ifgroup.by is not NULL.

size of the dots plotted ifgroup.by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable ifgroup.by is not NULL.

size of the dots plotted ifgroup.by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

whether to plot a pie chart or bar chart; value must be one of"bar" or"pie". Defaultis"bar"

whether to plot bar chart as total cell counts or percents, value must be one of"percent" or"count". Default is"percent".

meta data column to classify samples (default = "ident" and will useactive.ident).

meta data variable to use to split plots. Default is NULL which will plot across entire object.

number of columns in plot. Only valid ifsplit.by is not NULL.

Rotate x-axis labels 45 degrees (Default is FALSE). Only valid ifplot_type = "bar".

color palette to use for plotting.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Seurat object name.

name of meta.data column containing cluster values. Default isidentwhich defaults to current active.ident.

name of meta.data column containing sample group/condition variable.

name of meta.data column that contains sample ID information.

the size of points in plot (default is 1.5).

Rotate x-axis labels 45 degrees (Default is FALSE). Only valid ifplot_type = "bar".

color palette to use for plotting.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

name of the data.frame/tibble or path to CSV file containing cluster annotation.

name of column containing cluster names/numbers (default is "cluster").

name of column contain the cell type annotation (default is "cell_type").

path to the parent directory which contains all of the subdirectories of interest.

Seurat object name.

Feature from meta.data, assay features, or feature name shortcut to plot.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Feature to split plots by (i.e. "orig.ident").

number of bins to plot default is 250.

color to fill histogram bars, default is "dodgerblue".

Number of columns in plot layout.

optional, vector to use for plot title. Default is the name of thevariable being plotted.

assay to pull features from, default is active assay.

return list of accepted default shortcuts to provide tofeatures insteadof full name.

Seurat object name.

First feature to plot.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering genes per cell.

Plot line a potential high threshold for filtering genes per cell.

Plot line a potential low threshold for filtering feature1 per cell.

Plot line a potential high threshold for filtering feature1 per cell.

numerical value for thickness of cutoff lines, default is NULL.

vector of colors to use for plotting by identity.

Adjust point size for plotting.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident).Default is⁠@active.ident⁠.

Convert points to raster format. Default is NULL which will rasterize by default if greaterthan 100,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Name of assay to use, defaults to the active assay.

logical. Ifcolors_use = NULL, Whether or not to return plot using defaultggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Sets the seed if randomly shuffling the order of points (Default is 1).

Extra parameters passed toFeatureScatter.

Seurat object name.

First feature to plot.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering UMI per cell.

Plot line a potential high threshold for filtering UMI per cell.

Plot line a potential low threshold for filtering feature1 per cell.

Plot line a potential high threshold for filtering feature1 per cell.

numerical value for thickness of cutoff lines, default is NULL.

vector of colors to use for plotting by identity.

Adjust point size for plotting.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident).Default is⁠@active.ident⁠.

Convert points to raster format. Default is NULL which will rasterize by default if greaterthan 100,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Name of assay to use, defaults to the active assay.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Sets the seed if randomly shuffling the order of points (Default is 1).

Extra parameters passed toFeatureScatter.

Seurat object name.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering genes per cell.

Plot line a potential high threshold for filtering genes per cell.

Plot line a potential low threshold for filtering UMIs per cell.

Plot line a potential high threshold for filtering UMIs per cell.

numerical value for thickness of cutoff lines, default is NULL.

vector of colors to use for plotting by identity.

Name of continuous meta data variable to color points in plot by.(MUST be continuous variable i.e. "percent_mito").

The gradient color palette to use for plotting of meta variable (default isviridis "Plasma" palette with dark colors high).

Color to use for plotting values when ameta_gradient_low_cutoff isset (default is "lightgray").

Value to use as threshold for plotting.meta_gradient_name valuesbelow this value will be plotted usingmeta_gradient_na_color.

Cells to include on the scatter plot (default is all cells).

logical (default FALSE). Whether or not to return a plot layout with both theplot colored by identity and the meta data gradient plot.

logical, whether to plot the legend containing identities (left plot) whencombination = TRUE. Default is TRUE.

Passes size of points to bothFeatureScatter andgeom_point.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident).Default is⁠@active.ident⁠.

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore().Default is c(512, 512).

Name of assay to use, defaults to the active assay.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Sets the seed if randomly shuffling the order of points (Default is 1).

Extra parameters passed toFeatureScatter.

Seurat object name.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Numeric vector of length 1 or 2 to plot lines for potential low/high threshold for filtering.

Numeric vector of length 1 or 2 to plot lines for potential low/high threshold for filtering.

Numeric vector of length 1 or 2 to plot lines for potential low/high threshold for filtering.

The column name containing percent mitochondrial counts information. Default value is"percent_mito" which is default value created when usingAdd_Mito_Ribo().

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object name.

Feature from Meta Data to plot.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot Title.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting

logical, whether to plot median for each ident on the plot (Default is FALSE).

logical, whether to plot boxplot inside of violin (Default is FALSE).

Shape size for the median is plotted.

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object name.

Feature from Meta Data to plot.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot Title.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object name.

Plot Title.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

logical, whether to plot boxplot inside of violin (Default is FALSE).

Shape size for the median is plotted.

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

Name of assay to use, defaults to the active assay.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object name.

The column name containing percent mitochondrial counts information. Default value is"percent_mito" which is default value created when usingAdd_Mito_Ribo().

Plot Title.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object name.

Plot Title.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident);default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default ifgreater than 100,000 total points plotted (# Cells x # of features).

Name of assay to use, defaults to the active assay.

logical. Ifcolors_use = NULL, Whether or not to return plot usingdefault ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle ifcolors_use = NULL and number ofgroups plotted is greater than 36. Default = 123.

Extra parameters passed toVlnPlot.

Seurat object

number of cells per ident to use in down-sampling. This value must be less than orequal to the size of ident with fewest cells. Alternatively, can set to "min" which willuse the maximum number of barcodes based on size of smallest group.

The ident to use to group cells. Default is NULL which use current active.ident. .

logical, whether or not to return the results as list instead of vector, default isFALSE.

logical, if number of cells in identity is lower thannum_cells keep themaximum number of cells, default is FALSE. If FALSE will report error message ifnum_cells istoo high, if TRUE will subset cells with more thannum_cells to that value and those with lessthannum_cells will not be downsampled.

logical, whether to downsample to specific number of cells across whole object,instead of number of cells per identity, default is FALSE.

random seed to use for downsampling. Default is 123.

Seurat object to filter

Include features detected in at least this many cells. Will recalculate nCount and nFeaturemeta.data values as well.

Include cells where at least this many features are detected.

logical, override the Yes/No interactive check (see details). Default is FALSE; don't override.

logical, whether to print information on filtering parameters and number of cells/featuresremoved, Default is TRUE.

Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsvfiles provided by 10X.

A vector of file prefixes/names if specific samples are desired. Default isNULL andwill load all samples in given directory.

a set of sample names to use for each sample entry in returned list. IfNULL willset names to the file name of each sample.

Specify which column of genes.tsv or features.tsv to use for gene names; default is 2.

Specify which column of barcodes.tsv to use for cell names; default is 1.

Make feature names unique (default TRUE).

Remove trailing "-1" if present in all cell barcodes.

logical (default FALSE). Whether to use multiple cores when reading in data.Only possible on Linux based systems.

ifparallel = TRUE indicates the number of cores to use for multi-core processing.

logical (default FALSE) whether or not to merge samples into a single matrix or returnlist of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefixwill be taken fromsample_names.

path to the parent directory which contains all of the subdirectories of interest.

path from the parent directory to count matrix files for each sample.

logical (default TRUE) sets the secondary path variable to the default 10Xdirectory structure.

logical, whether samples were processed with Cell Rangermulti, default is FALSE.

a vector of sample directory names if only specific samples are desired. IfNULL willread in subdirectories in parent directory.

a set of sample names to use for each sample entry in returned list. IfNULL willset names to the subdirectory name of each sample.

logical (default FALSE) whether or not to use multi core processing to read in matrices.

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or returnlist of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefixwill be taken fromsample_names.

Extra parameters passed toRead10X.

Directory containing the .h5 files provided by 10X.

A vector of file prefixes/names if specific samples are desired. Default isNULL andwill load all samples in given directory.

a set of sample names to use for each sample entry in returned list. IfNULLwill set names to the file name of each sample.

a suffix and file extension shared by all samples.

logical (default FALSE). Whether to use multiple cores when reading in data.Only possible on Linux based systems.

ifparallel = TRUE indicates the number of cores to use for multicore processing.

logical (default FALSE) whether or not to merge samples into a single matrix or returnlist of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefixwill be taken fromsample_names.

Additional arguments passed toRead10X_h5

path to the parent directory which contains all of the subdirectories of interest.

path from the parent directory to count matrix files for each sample.

logical (default TRUE) sets the secondary path variable to the default 10Xdirectory structure.

logical, whether samples were processed with Cell Rangermulti, default is FALSE.

name of h5 file (including .h5 suffix). If all h5 files have same name (i.e. Cell Ranger output)then use full file name. By default function uses Cell Ranger name: "filtered_feature_bc_matrix.h5".If h5 files have sample specific prefixes (i.e. from Cell Bender) then use only the shared part of filename (e.g., "_filtered_out.h5").

a vector of sample directory names if only specific samples are desired. IfNULL willread in subdirectories in parent directory.

a set of sample names to use for each sample entry in returned list. IfNULL willset names to the subdirectory name of each sample.

logical (default FALSE). Whether or not to replace the barcode suffixes of matricesusingReplace_Suffix.

a vector of new suffixes to replace existing suffixes ifreplace_suffix = TRUE.SeeReplace_Suffix for more information. To remove all suffixes setnew_suffix_list = "".

logical (default FALSE) whether or not to use multi core processing to read in matrices.

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or returnlist of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefixwill be taken fromsample_names.

Extra parameters passed toRead10X_h5.

Seurat object name to add cNMF reduction

path and name of cNMF usage file

path and name of cNMF spectra file

name to use for reduction to be added, default is "cnmf".

key to use for reduction to be added, default is "cNMF_".

logical, whether to normalize the cNMF usage data, default is TRUE

assay to add reduction. Default is NULL and will use currentactive assay.

logical, whether to overwrite a reduction with the namereduction_name alreadypresent in reduction slot of given Seurat object.

Path to h5 file.

Label row names with feature names rather than ID numbers (default TRUE).

Make feature names unique (default TRUE).

Name of the group within H5 file that contains count data. This is onlyrequired if H5 file contains multiple subgroups and non-default names. Default isNULL.

Name of the slot contain feature names/ids. Must be one of:"features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".

path to the parent directory which contains all of the subdirectories of interest.

path from the parent directory to count matrix files for each sample.

logical (default TRUE). Will set the shared file name suffixcustom_name is NULL.

if file name was customized in CellBender then this parameter should contain the portionof file name that is shared across all samples. Must included the ".h5" extension as well.

a vector of sample directory names if only specific samples are desired. IfNULL willread in subdirectories in parent directory.

a set of sample names to use for each sample entry in returned list. IfNULL willset names to the subdirectory name of each sample. NOTE: unlesssample_list is specified this willrename files in the order they are read which will be alphabetical.

logical, whether or not the file has prefix identical to folder name. Default is TRUE.

Name of the group within H5 file that contains count data. This is onlyrequired if H5 file contains multiple subgroups and non-default names. Default isNULL.

Name of the slot contain feature names/ids. Must be one of:"features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".

logical (default FALSE). Whether or not to replace the barcode suffixes of matricesusingReplace_Suffix.

a vector of new suffixes to replace existing suffixes ifreplace_suffix = TRUE.SeeReplace_Suffix for more information. To remove all suffixes setnew_suffix_list = "".

logical (default FALSE) whether or not to use multi core processing to read in matrices.

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or returnlist of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefixwill be taken fromsample_names.

Extra parameters passed toRead_CellBender_h5_Mat.

Directory containing the .h5 files output by CellBender.

logical (default TRUE). Will set the shared file name suffix ifcustom_name is NULL.

if file name was customized in CellBender then this parameter should contain the portionof file name that is shared across all samples. Must included the ".h5" extension as well.

a vector of sample names if only specific samples are desired. IfNULL willread in all files withindata_dir directory.

a set of sample names to use for each sample entry in returned list. IfNULL willset names to the subdirectory name of each sample.

Name of the group within H5 file that contains count data. This is onlyrequired if H5 file contains multiple subgroups and non-default names. Default isNULL.

Name of the slot contain feature names/ids. Must be one of:"features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".

logical (default FALSE) whether or not to use multi core processing to read in matrices

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or returnlist of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefixwill be taken fromsample_names.

Extra parameters passed toRead_CellBender_h5_Mat.

Directory containing the files.

The file suffix of the individual files. Must be the same across all files beingimported. This is used to detect files to import and their GEO IDs.

logical. Whether gene IDs are present in first column or in row names ofdelimited file. If TRUE will move the first column to row names before creating final matrix.Default is TRUE.

a vector of samples within directory to read in (can be either with orwithoutfile_suffix seefull_names). If NULL will read in all subdirectories.

logical (default FALSE). Whether or not thesample_list vector includes the file suffix.IfFALSE the function will add suffix based onfile_suffix parameter.

a set of sample names to use for each sample entry in returned list.IfNULL will set names to the directory name of each sample.

Is the barcode suffix a period and should it be changed to "-". Default (FALSE;barcodes will be left identical to their format in input files.). If TRUE "." in barcode suffix willbe changed to "-".

logical (default FALSE). Whether to use multiple cores when reading in data.Only possible on Linux based systems.

ifparallel = TRUE indicates the number of cores to use for multicore processing.