updated subset cell functionality to all plots

SGDDNB · Jul 6, 2021 · 71111ad · 71111ad
1 parent 2f3e731
commit 71111ad
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Showing 10 changed files with 261 additions and 197 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ShinyCell
 Type: Package
 Title: Shiny Interactive Web Apps for Single-Cell Data
-Version: 2.0.0
+Version: 2.1.0
 Author: John F. Ouyang
 Maintainer: John F. Ouyang <john.f.ouyang@gmail.com>
 Description: Shiny apps for interactive exploration of single-cell data

diff --git a/R/makeShinyApp.R b/R/makeShinyApp.R
@@ -33,6 +33,10 @@
 #'   page, year, doi, link. See example below. 
 #' @param shiny.dir specify directory to create the shiny app in. Default is 
 #'   to create a new directory named "shinyApp"
+#' @param enableSubset specify whether to enable "Toggle to subset cells" 
+#'   functionality in the shiny app. Default is to enable this functionality
+#' @param defPtSiz specify default point size for single cells. For example, a 
+#'   smaller size can be used if you have many cells in your dataset
 #' @param ganalytics Google analytics tracking ID (e.g. "UA-123456789-0")
 #' @param default.gene1 specify primary default gene to show
 #' @param default.gene2 specify secondary default gene to show
@@ -71,7 +75,7 @@ makeShinyApp <- function(
   obj, scConf, gex.assay = NA, gex.slot = c("data", "scale.data", "counts"), 
   gene.mapping = FALSE, 
   shiny.title = "scRNA-seq shiny app", shiny.footnotes = "",
-  shiny.dir = "shinyApp/", ganalytics = NA,
+  shiny.dir = "shinyApp/", enableSubset = TRUE, defPtSiz = 1.25, ganalytics=NA,
   default.gene1 = NA, default.gene2 = NA, default.multigene = NA, 
   default.dimred = NA){
 
@@ -84,6 +88,7 @@ makeShinyApp <- function(
                  default.gene1, default.gene2, default.multigene, default.dimred)
   makeShinyCodes(shiny.title = shiny.title, shiny.footnotes = shiny.footnotes,
                  shiny.prefix = "sc1", shiny.dir = shiny.dir, 
+                 enableSubset = enableSubset, defPtSiz = defPtSiz,
                  ganalytics = ganalytics)
 
 }

diff --git a/R/makeShinyCodes.R b/R/makeShinyCodes.R
@@ -13,6 +13,10 @@
 #'   page, year, doi, link. See example below. 
 #' @param shiny.prefix specify file prefix 
 #' @param shiny.dir specify directory to create the shiny app in
+#' @param enableSubset specify whether to enable "Toggle to subset cells" 
+#'   functionality in the shiny app. Default is to enable this functionality
+#' @param defPtSiz specify default point size for single cells. For example, a 
+#'   smaller size can be used if you have many cells in your dataset
 #' @param ganalytics Google analytics tracking ID (e.g. "UA-123456789-0")
 #'
 #' @return server.R and ui.R required for shiny app
@@ -37,7 +41,13 @@
 #'
 #' @export
 makeShinyCodes <- function(shiny.title, shiny.footnotes,
-                           shiny.prefix, shiny.dir, ganalytics = NA){
+                           shiny.prefix, shiny.dir, 
+                           enableSubset = TRUE, defPtSiz = 1.25,
+                           ganalytics = NA){
+  subst = "#"
+  if(enableSubset){subst = ""}
+  defPtSiz = as.character(defPtSiz)
+
   if(packageVersion("readr") >= "1.4.0"){
     ### Write code for server.R
     fname = paste0(shiny.dir, "/server.R")
@@ -46,7 +56,7 @@ makeShinyCodes <- function(shiny.title, shiny.footnotes,
         "ggrepel","hdf5r","ggdendro","gridExtra")), file = fname)
     readr::write_file(wrSVload(shiny.prefix), append = TRUE, file = fname)
     readr::write_file(wrSVfix(), append = TRUE, file = fname)
-    readr::write_file(wrSVmain(shiny.prefix), append = TRUE, file = fname)
+    readr::write_file(wrSVmain(shiny.prefix, subst), append = TRUE, file = fname)
     readr::write_file(wrSVend(), append = TRUE, file = fname)
 
 
@@ -56,7 +66,7 @@ makeShinyCodes <- function(shiny.title, shiny.footnotes,
       c("shiny","shinyhelper","data.table","Matrix","DT","magrittr")), file = fname)
     readr::write_file(wrUIload(shiny.prefix), append = TRUE, file = fname)
     readr::write_file(wrUIsingle(shiny.title, ganalytics), append = TRUE, file = fname)
-    readr::write_file(wrUImain(shiny.prefix), append = TRUE, file = fname)
+    readr::write_file(wrUImain(shiny.prefix, subst, defPtSiz), append = TRUE, file = fname)
     readr::write_file(glue::glue(', \n'), append = TRUE, file = fname)
     readr::write_file(wrUIend(shiny.footnotes), append = TRUE, file = fname)
 
@@ -75,7 +85,7 @@ makeShinyCodes <- function(shiny.title, shiny.footnotes,
         "ggrepel","hdf5r","ggdendro","gridExtra")), path = fname)
     readr::write_file(wrSVload(shiny.prefix), append = TRUE, path = fname)
     readr::write_file(wrSVfix(), append = TRUE, path = fname)
-    readr::write_file(wrSVmain(shiny.prefix), append = TRUE, path = fname)
+    readr::write_file(wrSVmain(shiny.prefix, subst), append = TRUE, path = fname)
     readr::write_file(wrSVend(), append = TRUE, path = fname)
 
 
@@ -85,7 +95,7 @@ makeShinyCodes <- function(shiny.title, shiny.footnotes,
       c("shiny","shinyhelper","data.table","Matrix","DT","magrittr")), path = fname)
     readr::write_file(wrUIload(shiny.prefix), append = TRUE, path = fname)
     readr::write_file(wrUIsingle(shiny.title, ganalytics), append = TRUE, path = fname)
-    readr::write_file(wrUImain(shiny.prefix), append = TRUE, path = fname)
+    readr::write_file(wrUImain(shiny.prefix, subst, defPtSiz), append = TRUE, path = fname)
     readr::write_file(glue::glue(', \n'), append = TRUE, path = fname)
     readr::write_file(wrUIend(shiny.footnotes), append = TRUE, path = fname)
 

diff --git a/R/makeShinyCodesMulti.R b/R/makeShinyCodesMulti.R
@@ -16,6 +16,12 @@
 #' @param shiny.headers specify the tab header names for each dataset. Length 
 #'   must match that of \code{shiny.prefix}
 #' @param shiny.dir specify directory to create the shiny app in
+#' @param enableSubset specify whether to enable "Toggle to subset cells" 
+#'   functionality in the shiny app. Default is to enable this functionality
+#' @param defPtSiz specify default point size for single cells. For example, a 
+#'   smaller size can be used if you have many cells in your dataset. A single 
+#'   value can be specified to set the point size for all datasets. Otherwise,
+#'   users have to specify one value for each dataset
 #' @param ganalytics Google analytics tracking ID (e.g. "UA-123456789-0")
 #'
 #' @return server.R and ui.R required for shiny app
@@ -36,18 +42,25 @@
 #'   doi     = "10.1038/s41586-020-2734-6",
 #'   link    = "https://www.nature.com/articles/s41586-020-2734-6")
 #' makeShinyCodes(shiny.title = "scRNA-seq shiny app", shiny.footnotes = "",
-#'                shiny.prefix = c("sc1", "sc2"), 
+#'                shiny.prefix = c("sc1", "sc2"), defPtSiz = c(1.25, 1.5),
 #'                shiny.headers = c("dataset1", "dataset2"),
 #'                shiny.dir = "shinyApp/")
 #'                
 #' @export
 makeShinyCodesMulti <- function(shiny.title, shiny.footnotes,
                                 shiny.prefix, shiny.headers, shiny.dir, 
+                                enableSubset = TRUE, defPtSiz = 1.25,
                                 ganalytics = NA){
   ### Checks
   if(length(shiny.prefix) != length(shiny.headers)){
     stop("length of shiny.prefix and shiny.headers does not match!")
   }
+  subst = "#"
+  if(enableSubset){subst = ""}
+  if(length(shiny.prefix) != length(defPtSiz)){
+    defPtSiz = rep(defPtSiz[1], length(shiny.prefix))
+  }
+  defPtSiz = as.character(defPtSiz)
 
   if(packageVersion("readr") >= "1.4.0"){
     ### Write code for server.R
@@ -60,7 +73,7 @@ makeShinyCodesMulti <- function(shiny.title, shiny.footnotes,
     }
     readr::write_file(wrSVfix(), append = TRUE, file = fname)
     for(i in shiny.prefix){
-      readr::write_file(wrSVmain(i), append = TRUE, file = fname)
+      readr::write_file(wrSVmain(i, subst), append = TRUE, file = fname)
     }
     readr::write_file(wrSVend(), append = TRUE, file = fname)
 
@@ -77,7 +90,8 @@ makeShinyCodesMulti <- function(shiny.title, shiny.footnotes,
       hhh = shiny.headers[i]
       readr::write_file(glue::glue('navbarMenu("{hhh}",'), 
                         append = TRUE, file = fname)
-      readr::write_file(wrUImain(shiny.prefix[i]), append = TRUE, file = fname)
+      readr::write_file(wrUImain(shiny.prefix[i], subst, defPtSiz[i]), 
+                        append = TRUE, file = fname)
       readr::write_file(glue::glue('), \n\n\n'), append = TRUE, file = fname)
     }
     readr::write_file(wrUIend(shiny.footnotes), append = TRUE, file = fname)
@@ -100,7 +114,7 @@ makeShinyCodesMulti <- function(shiny.title, shiny.footnotes,
     }
     readr::write_file(wrSVfix(), append = TRUE, path = fname)
     for(i in shiny.prefix){
-      readr::write_file(wrSVmain(i), append = TRUE, path = fname)
+      readr::write_file(wrSVmain(i, subst), append = TRUE, path = fname)
     }
     readr::write_file(wrSVend(), append = TRUE, path = fname)
 
@@ -117,7 +131,8 @@ makeShinyCodesMulti <- function(shiny.title, shiny.footnotes,
       hhh = shiny.headers[i]
       readr::write_file(glue::glue('navbarMenu("{hhh}",'), 
                         append = TRUE, path = fname)
-      readr::write_file(wrUImain(shiny.prefix[i]), append = TRUE, path = fname)
+      readr::write_file(wrUImain(shiny.prefix[i], subst, defPtSiz[i]), 
+                        append = TRUE, path = fname)
       readr::write_file(glue::glue('), \n\n\n'), append = TRUE, path = fname)
     }
     readr::write_file(wrUIend(shiny.footnotes), append = TRUE, path = fname)