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Commit389d513

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Updating vignette and code formatting
1 parent3ca9ceb commit389d513

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50 files changed

+1157
-135
lines changed

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50 files changed

+1157
-135
lines changed

‎R/mod_evaluation.R‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,8 @@ server_evaluation <- function(id, selected_data, clusters) {
3838
metric_results<- compute_metric(selected_data(),
3939
clusters(),
4040
input$evaluation_selected)
41-
validate(need(all(!is.na(metric_results)),"Metric not evaluated for current data"))
41+
validate(need(all(!is.na(metric_results)),
42+
"Metric not evaluated for current data"))
4243
optimal_k<- optimal_score(metric_results$score,
4344
method=input$evaluation_highlight)
4445

‎R/mod_gapstat.R‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,8 @@ server_gapstat <- function(id, selected_data, clusters) {
4949
df<- selected_data()
5050
clustered_data<- clusters()
5151
})
52-
validate(need(input$gap_B>0,"Bootstrap samples must be greater than 0."))
52+
validate(need(input$gap_B>0,
53+
"Bootstrap samples must be greater than 0."))
5354
compute_gapstat(df,clustered_data,input$gap_B)
5455
})
5556

‎R/mod_pca.R‎

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,10 @@ ui_pca <- function() {
55
splitLayout(
66
verticalLayout(
77
fluidRow(
8-
column(6,selectizeInput(ns("pca_xaxis"),label="X axis:",choices=NULL)),
9-
column(6,selectizeInput(ns("pca_yaxis"),label="Y axis:",choices=NULL))),
8+
column(6,selectizeInput(ns("pca_xaxis"),
9+
label="X axis:",choices=NULL)),
10+
column(6,selectizeInput(ns("pca_yaxis"),
11+
label="Y axis:",choices=NULL))),
1012
plotOutput(ns("pca_plot"),width="100%",height="400px")
1113
),
1214
plotOutput(ns("drivers_plot"),width="100%",height="auto"),
@@ -26,14 +28,17 @@ server_pca <- function(id, selected_data, cluster_labels, cluster_colors) {
2628
observeEvent(pca_data(), {
2729
pca_res<- pca_data()
2830
pca_dims<- colnames(pca_res$x)
29-
updateSelectizeInput(session,"pca_xaxis",choices=pca_dims,selected="PC1")
30-
updateSelectizeInput(session,"pca_yaxis",choices=pca_dims,selected="PC2")
31+
updateSelectizeInput(session,"pca_xaxis",
32+
choices=pca_dims,selected="PC1")
33+
updateSelectizeInput(session,"pca_yaxis",
34+
choices=pca_dims,selected="PC2")
3135
})
3236

3337
output$pca_plot<- renderPlot({
3438
req(input$pca_xaxis)
3539
req(input$pca_yaxis)
36-
pca_scatterplot(pca_data(), cluster_labels(),cluster_colors,input$pca_xaxis,input$pca_yaxis)
40+
pca_scatterplot(pca_data(), cluster_labels(),
41+
cluster_colors,input$pca_xaxis,input$pca_yaxis)
3742
})
3843

3944
output$drivers_plot<- renderPlot({

‎R/mod_significance.R‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -58,7 +58,8 @@ server_significance <- function(id, all_data, cluster_labels, cluster_colors,
5858
}
5959
else {
6060
all_df$Cluster<-clusters
61-
t_test_formula<-stats::as.formula(paste(input$signif_var," ~ Cluster"))
61+
t_test_formula<-
62+
stats::as.formula(paste(input$signif_var," ~ Cluster"))
6263
stats::t.test(t_test_formula,data=all_df)
6364
}
6465
})

‎R/mod_table.R‎

Lines changed: 0 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -81,27 +81,6 @@ server_table <- function(id, all_data, selected_data, cluster_labels, nclusters)
8181
new_data(updated_data)
8282

8383
})
84-
# new_data <- eventReactive(input$remove_subjects, {
85-
# isolate({
86-
# all_df <- all_data()
87-
# })
88-
# browser()
89-
# remove_selected_rows(all_df,
90-
# cluster_labels(),
91-
# input$clusters_selection,
92-
# input$clusters_table_rows_selected)
93-
# # this updates all_data after removing rows
94-
# })
95-
#
96-
# new_data <- eventReactive(input$keep_subjects, {
97-
# isolate({
98-
# all_df <- all_data()
99-
# })
100-
# keep_selected_rows(all_df,
101-
# cluster_labels(),
102-
# input$clusters_selection)
103-
# })
104-
10584

10685
new_data
10786

‎R/plot.R‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,8 @@ facet_boxplot <- function(df, x, y, facet_var = NULL,
2020
shape<- match.arg(shape)
2121
if (!x%in% colnames(df)) stop("x variable not found in data frame")
2222
if (!y%in% colnames(df)) stop("y variable not found in data frame")
23-
if (!is.null(facet_var)&& (!facet_var%in% colnames(df))) stop("facet_var variable not found in data frame")
23+
if (!is.null(facet_var)&& (!facet_var%in% colnames(df)))
24+
stop("facet_var variable not found in data frame")
2425
p<- ggplot(df, aes(x=.data[[x]],fill=.data[[x]]))+
2526
theme_bw()+
2627
theme(panel.grid.major.x= element_blank(),
@@ -60,7 +61,8 @@ facet_boxplot <- function(df, x, y, facet_var = NULL,
6061

6162
#' Plot boxplots with clusters
6263
#'
63-
#' This is a convenience wrapper function for `facet_boxplot()`. Combined with `annotate_clusters()`, it
64+
#' This is a convenience wrapper function for `facet_boxplot()`.
65+
#' Combined with `annotate_clusters()`, it
6466
#' doesn't require specifying axes in `facet_boxplot()`.
6567
#'
6668
#' @param annotated_data data frame returned by `annotate_clusters()`
@@ -111,7 +113,8 @@ line_plot <- function(df, x, y, xintercept = NULL) {
111113
#' @param cluster_colors a list of colors to match the cluster labels
112114
#'
113115
#' @noRd
114-
pca_scatterplot<-function(pcres,cluster_labels,cluster_colors,xdim="PC1",ydim="PC2") {
116+
pca_scatterplot<-
117+
function(pcres,cluster_labels,cluster_colors,xdim="PC1",ydim="PC2") {
115118
pc_df<- as.data.frame(pcres$x)
116119
var_explained<- round(pcres$sdev/ sum(pcres$sdev)*100,2)
117120
pc_labels<-stats::setNames(paste0(colnames(pc_df),

‎R/server.R‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,8 @@ app_server <- function(input, output, session) {
7575

7676
# Update UI ----
7777
selected_numeric<- reactive({
78-
validate(need(!is.null(input$selected_numeric),"No features have been selected"))
78+
validate(need(!is.null(input$selected_numeric),
79+
"No features have been selected"))
7980
input$selected_numeric
8081
})
8182

@@ -118,8 +119,10 @@ app_server <- function(input, output, session) {
118119
})
119120

120121
scaled_data<- reactive({
121-
scaled_mat<- scale_data(selected_data(),input$scaling)
122-
isolate({ rownames(scaled_mat)<- all_data()$ID })
122+
if (input$distance_method!="Binary") {
123+
scaled_mat<- scale_data(selected_data(),input$scaling)
124+
isolate({ rownames(scaled_mat)<- all_data()$ID })
125+
}elsescaled_mat<- selected_data()
123126
scaled_mat
124127
})
125128

‎README.Rmd‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -53,5 +53,7 @@ To run the app once the package is installed:
5353

5454
```{r example, eval = FALSE}
5555
library(visxhclust)
56+
# Increases max file size to 30 MB
57+
options(shiny.maxRequestSize = 30*1024^2
5658
run_app()
5759
```

‎README.md‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -71,5 +71,7 @@ To run the app once the package is installed:
7171

7272
```r
7373
library(visxhclust)
74+
# Increases max file size to 30 MB
75+
options(shiny.maxRequestSize=30*1024^2
7476
run_app()
7577
```

‎dev/dev_init.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@
4141
#usethis::use_vignette("visxhclust")
4242

4343
#usethis::use_testthat()
44-
usethis::use_github_actions()
44+
#usethis::use_github_actions()
4545

4646
devtools::document()
4747
pkgdown::build_site()

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