added side by side dimension and feature plots

README.md

@@ -7,6 +7,6 @@ Date: September 25, 2023
 
 Description: Shiny app visualization of scRNA-seq data analyzed by the Morrison Lab.
 
-Input: An .rdata file of a Seurat object with required variables.
+Input: An .rdata file of a Seurat object analyzed through the Morrison Lab's scRNA-seq data analysis pipeline.
 
 Output: Violin plots, UMAPs, heatmaps, dot plots, ridge plots, and scatter plots of selected genes, samples, and clusters.

astrocyte_pkg.yml

@@ -7,7 +7,7 @@
 # -----------------------------------------------------------------------------
 
 # A unique identifier for the workflow package, text/underscores only
-name: 'scRNA_Astrocyte'
+name: 'scVizIt'
 # Who wrote this?
 author: 'Brandon Chen and Sylvia Zhao'
 # A contact email address for questions

docs/index.md

-# Astrocyte scRNA Workflow Package
+# Astrocyte scVizIt Workflow Package
 
 This is an vizapp for the visualization of scRNA-seq data.
 
 ## The Workflow
 
-The workflow `workflow/main.nf` has simply copies the input data files to the output directory so they are available to the vizapp.
+The workflow `workflow/main.nf` simply copies the input data files to the output directory so they are available to the vizapp. The input file should be an .rdata file generated by the Morrison Lab's scRNA-seq data analysis pipeline. 
+
+For more information, please contact Zhiyu.Zhao@utsouthwestern.edu
 
 ## Parameters
 
-There is a single parameter `scData`. This provides 1 or more files that the
-workflow should run on.
+There is a single parameter `scData`. This provides up to 5 files that the
+workflow should run on. 
 
 ## Questions
 

vizapp/shinyapp/server.R

@@ -206,9 +206,9 @@ server <- function(input, output, session) {
   dimFigure <- eventReactive(input$apply_changes,{
   	group.by=input$group
   	label=input$label #new
-  	reduction=input$reduction_dim #new
+  	reduction=input$reduction #new
 
-  	if (input$reduction_dim == 'tsne'){
+  	if (input$reduction == 'tsne'){
   		if (class(try(samples.integrated[['tsne']]))=='try-error') {samples.integrated=RunTSNE(samples.integrated)}
   	}
 

vizapp/shinyapp/ui.R

@@ -164,44 +164,24 @@ conditionalPanel(condition= "output.loading",
 			h5("Files uploaded must not contain PHI or other privacy sensitive information without prior approval.",inline=T),
 			tabsetPanel(type = "tabs",
 
-				tabPanel("Dimension Plot",
-					checkboxInput("label",
-						"Toggle Labels",
-						value = TRUE),
-					selectInput("reduction_dim",
-						"Type of Reduction",
-						choices=c("UMAP"="umap",
-							"t-SNE"="tsne",
-							"PCA"="pca"),
-						selected=c("umap")
-						),
-					plotOutput(
-						"dimension",
-						width = "100%"
-                             ),
-					column(12, 
-						downloadButton("download7",
-							"Download Dimension Plot"))
-					),
-				tabPanel("Feature Plot",
+				tabPanel("Dimensional Reduction Plot",
 					checkboxInput("split_plots",
 						"Split Feature Plots by Group",
 						value = FALSE),
+					checkboxInput("label",
+						"Toggle Labels",
+						value = TRUE),
 					selectInput("reduction",
 						"Type of Reduction",
 						choices=c("UMAP"="umap",
 							"t-SNE"="tsne",
 							"PCA"="pca"),
-						selected=c("umap")
-						),
-					plotOutput(
-						"plot1",
-						width = "100%"
-                             # dblclick = "umap_dbl",
-                             # brush = brushOpts(id = "brush",resetOnNew = TRUE)
-                             ),
-
-					column(12, 
+						selected=c("umap")),
+                    splitLayout(plotOutput("dimension"), plotOutput("plot1")),
+					column(6, 
+						downloadButton("download7",
+							"Download Dimension Plot")),
+					column(6, 
 						downloadButton("download2",
 							"Download Feature Plot"))
 					),