Movatterモバイル変換

[0]ホーム
URL:

Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

 Sign up
Appearance settings

Visualising single-cell trajectories, including comparisons between two models 📈

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md
NotificationsYou must be signed in to change notification settings

dynverse/dynplot

Repository files navigation


ℹ️ Tutorials    ℹ️ Referencedocumentation

Visualise a single-cell trajectory as a graph or dendrogram, as adimensionality reduction or heatmap of the expression data, or acomparison between two trajectories as a pairwise scatterplot ordimensionality reduction projection.

Here’s a summary of the different plotting functions for visualisingsingle-cell trajectories.

library(tidyverse)library(dyno)# get trajectorydata(example_bifurcating)trajectory<-example_bifurcating %>% add_root()# gather some prior informationgrouping<-trajectory$prior_information$groups_idgroups<- tibble(group_id=trajectory$milestone_ids,color=dynplot:::milestone_palette_list$auto(length(group_id)))features_oi<- apply(as.matrix(trajectory$counts),2,sd) %>% sort() %>% names() %>% tail(10)feature_oi<-features_oi[[10]]

plot_dendro(): Plot a trajectory as a dendrogram

patchwork::wrap_plots(  plot_dendro(trajectory)+ labs(title="Topology"),  plot_dendro(trajectory,"milestone")+ labs(title="Ordering"),  plot_dendro(trajectory,grouping=grouping,groups=groups)+ labs(title="Grouping/clustering"),  plot_dendro(trajectory,feature_oi=feature_oi)+ labs(title="Expression of\na single gene"),  plot_dendro(trajectory,"pseudotime")+ labs(title="Pseudotime"),byrow=TRUE,ncol=3)& theme(legend.position="none")

plot_onedim(): Plot a trajectory as a one-dimensional set of connected segments

patchwork::wrap_plots(  plot_onedim(trajectory)+ labs(title="Topology"),  plot_onedim(trajectory,"milestone")+ labs(title="Ordering"),  plot_onedim(trajectory,grouping=grouping,groups=groups)+ labs(title="Grouping/clustering"),  plot_onedim(trajectory,feature_oi=feature_oi)+ labs(title="Expression of\na single gene"),  plot_onedim(trajectory,"pseudotime")+ labs(title="Pseudotime"),byrow=TRUE,ncol=2)& theme(legend.position="none")

plot_graph(): Plot a trajectory and cellular positions as a graph

patchwork::wrap_plots(  plot_graph(trajectory)+ labs(title="Topology"),  plot_graph(trajectory,"milestone")+ labs(title="Ordering"),  plot_graph(trajectory,grouping=grouping,groups=groups)+ labs(title="Grouping/clustering"),  plot_graph(trajectory,feature_oi=feature_oi)+ labs(title="Expression of\na single gene"),  plot_graph(trajectory,"pseudotime")+ labs(title="Pseudotime"),byrow=TRUE,ncol=3)& theme(legend.position="none")

plot_dimred(): Plot a trajectory in a (given) dimensionality reduction

patchwork::wrap_plots(  plot_dimred(trajectory)+ labs(title="Topology"),  plot_dimred(trajectory,"milestone")+ labs(title="Ordering"),  plot_dimred(trajectory,grouping=grouping,groups=groups)+ labs(title="Grouping/clustering"),  plot_dimred(trajectory,feature_oi=feature_oi)+ labs(title="Expression of\na single gene"),  plot_dimred(trajectory,"pseudotime")+ labs(title="Pseudotime"),byrow=TRUE,ncol=3)& theme(legend.position="none")

plot_heatmap(): Plot expression data along a trajectory

In addition, you can also plot the expression of genes along thetrajectory as a heatmap.

plot_heatmap(trajectory,grouping=trajectory$prior_information$grouping_assignment)

plot_linearised_comparison(): Compare two trajectories as a pseudotime scatterplot

You can compare multiple trajectories (for the same cells) by creating ascatterplot between the two trajectories.

prediction<- infer_trajectory(trajectory, ti_comp1())#> v0.9.9.01: Pulling from dynverse/ti_comp1#> 844c33c7e6ea: Pulling fs layer#> 4f11e4e30170: Pulling fs layer#> a9724dff2655: Pulling fs layer#> f5f3a048c9c3: Pulling fs layer#> a53c4db932de: Pulling fs layer#> bd5da474b8ba: Pulling fs layer#> be9b916e18e7: Pulling fs layer#> b8b469f67972: Pulling fs layer#> e33132a1a81b: Pulling fs layer#> 32bd550d2fc1: Pulling fs layer#> a828ddf00b38: Pulling fs layer#> d97023e2f782: Pulling fs layer#> 84d8340a282e: Pulling fs layer#> be9b916e18e7: Waiting#> e33132a1a81b: Waiting#> 32bd550d2fc1: Waiting#> a828ddf00b38: Waiting#> a53c4db932de: Waiting#> b8b469f67972: Waiting#> f5f3a048c9c3: Waiting#> bd5da474b8ba: Waiting#> d97023e2f782: Waiting#> 844c33c7e6ea: Verifying Checksum#> 844c33c7e6ea: Download complete#> 844c33c7e6ea: Pull complete#> f5f3a048c9c3: Verifying Checksum#> f5f3a048c9c3: Download complete#> a53c4db932de: Verifying Checksum#> a53c4db932de: Download complete#> bd5da474b8ba: Verifying Checksum#> bd5da474b8ba: Download complete#> be9b916e18e7: Download complete#> 4f11e4e30170: Verifying Checksum#> 4f11e4e30170: Download complete#> 4f11e4e30170: Pull complete#> e33132a1a81b: Verifying Checksum#> e33132a1a81b: Download complete#> a9724dff2655: Verifying Checksum#> a9724dff2655: Download complete#> 32bd550d2fc1: Verifying Checksum#> 32bd550d2fc1: Download complete#> a9724dff2655: Pull complete#> f5f3a048c9c3: Pull complete#> a53c4db932de: Pull complete#> bd5da474b8ba: Pull complete#> be9b916e18e7: Pull complete#> a828ddf00b38: Verifying Checksum#> a828ddf00b38: Download complete#> 84d8340a282e: Verifying Checksum#> 84d8340a282e: Download complete#> d97023e2f782: Download complete#> b8b469f67972: Verifying Checksum#> b8b469f67972: Download complete#> b8b469f67972: Pull complete#> e33132a1a81b: Pull complete#> 32bd550d2fc1: Pull complete#> a828ddf00b38: Pull complete#> d97023e2f782: Pull complete#> 84d8340a282e: Pull complete#> Digest: sha256:012b3bfef2250767bcd3f3b389ebff82d4a2dc23d39b1bdadf7076e23b833680#> Status: Downloaded newer image for dynverse/ti_comp1:v0.9.9.01#> docker.io/dynverse/ti_comp1:v0.9.9.01trajectory$id<-"Bifurcating"prediction$id<-"Linear"plot_linearised_comparison(trajectory,prediction)

Latest changes

Check outnews(package = "dynwrap") orNEWS.md for a fulllist of changes.

Recent changes in dynplot 1.1.1

  • BUG FIXproject_waypoints_coloured(): Fix refactoring issue “Mustsupply a symbol or a string as argument” (#54).

  • BUG FIXproject_waypoints_coloured(): Fix wrong results whenprojecting waypoint segments (#54 bis).

Recent changes in dynplot 1.1.0

Initial release on CRAN.

  • MINOR CHANGE: Addarrow parameter to all plot functions.

  • BUG FIX: Apply fixes for new versions of tibble, tidyr, and ggraph.

  • BUG FIXoptimise_order(): Fix problem where GA::ga() wouldn’t runon milestone networks with 1 or 4 edges.

  • BUG FIXlinearise_cells(): Fix ordering issue whenequal_cell_width isTRUE.

  • MINOR CHANGE: Clean imports and supposed undefined variables.

  • MINOR CHANGEplot_dendro(): Allow plotting of disconnected graphs(#32). This assumes thatdynwrap::add_root(traj, root_milestone_id = c(...)) has beencalled properly.

  • DOCUMENTATION: Extend documentation on usage of parameters and theexpected output values of functions.

About

Visualising single-cell trajectories, including comparisons between two models 📈

Topics

Resources

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md

Stars

Watchers

Forks

Packages

No packages published

Contributors4

  •  
  •  
  •  
  •  

Languages

[8]ページ先頭
©2009-2025 Movatter.jp