Minor fixes/cleanup

Author: fercrcode

code/2-umap.py

@@ -100,14 +100,6 @@
 print(f"\n Number of markers used: {len(all_together_vs_marks.columns)}")
 
 
-#~~~~~~~~~~~~~~~~~~~Optional: z-score transformation~~~~~~~~~~~~~~~~~~~~~~~~~~#
-# Z-SCORE: Not used now, interactive inplementation on later stages of the pipeline
-# z-score transformation (for the Organoid Methods Paper, only applied to supplementary figure 1)
-# all_together_vs_marks.head()
-# all_together_vs_marks = all_together_vs_marks.apply(zscore)
-# all_together_vs_marks.head()
-
-
 #~~~~~~~~~~~~~~~~~~~~~~~~~~Perform  and save UMAP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 #Define UMAP parameters
 

code/5v2-pca.py

@@ -1,5 +1,5 @@
 ###############################################################################
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#~Heatmaps~#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#~PCA~#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ###############################################################################
 #Calculate and plot PCAs on EMD and DREMI scores
 import os
@@ -8,11 +8,9 @@
 
 from aux.aux_functions import yes_or_NO
 
-#2 options for the PCA plots:
-    #Either run basic PCA on R and plot in shiny app (less graphical customisation, simpler plots)
-    #Leverage PCA shiny apps. 
-        #PCAshiny from Factoshiny -> Very basic
-        #Interactive PCA Explorer
+#Import yes or no question to choose the different plotings
+#Run the separate R shiny apps accordingly
+#Simultaneous emd and DREMI should both be possible since the ports are random
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I/O~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 base_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))

code/aux/aux4_dremi.py

@@ -8,6 +8,7 @@
 import scprep
 
 
+# EXPERIMENTAL #
 # find outliers for both marker_x and marker_y based on cufoffs of standard deviations
 # return the number of outliers and a dataframe after outlier removal
 # update the df_info_dict with the number of outliers

code/aux/aux5v1_dremi.R

@@ -13,9 +13,11 @@ if(length(new.packages)) install.packages(new.packages, repos = "http://cran.us.
 #Load packages
 lapply(list.of.packages, require, character.only = TRUE)
 
+#FUTURE WORK: Look into ComplexHeatmap (group similar DREMI patterns)
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~DATA SETUP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
-#Make sure no_norm is like this and marker_marker, not marker-marker -> check dremi script for populatiog the column itself, although i don't think that will pose a problem here in R
+#Make sure no_norm is like this and marker_marker, not marker-marker -> 
+#check dremi script for populatiog the column itself, although i don't think that will pose a problem here in R
 dremi_info <- read_tsv(args)
 minx <- min(dremi_info$with_outliers_arcsinh_DREMI_score)
 maxx <- max(dremi_info$with_outliers_arcsinh_DREMI_score)
@@ -33,7 +35,7 @@ initial_dremi <- dremi_info %>% ggplot(aes(
 ###############################################################################
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#~UI~#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ###############################################################################
-# Define UI for application that draws a histogram
+
 ui <- fluidPage(
 
     # Application title
@@ -59,12 +61,12 @@ ui <- fluidPage(
 ###############################################################################
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#~Server~#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ###############################################################################
-# Define server logic required to draw a histogram
+
 server <- function(input, output, session) {
 
     output$out6 <- renderPrint(input$in6)
 
-    output$trendPlot <- renderPlotly({
+    output$trendPlot <- renderPlotly({ #Process input data and make plotly heatmap
         if (!is.null(input$in6) & !is.null(input$in12)) {
             data_to_plot <- dremi_info %>% filter(str_detect(marker_x_marker_y, input$in6)) %>% filter(file_origin %in% input$in12)
             data_to_plot$file_origin <- as.factor(data_to_plot$file_origin) %>% fct_relevel(input$in12)
@@ -95,7 +97,7 @@ server <- function(input, output, session) {
             ) %>% layout(height = 800) # %>% layout(height = 1400, width = 1200)
         )
     })
-    output$foo <- downloadHandler(
+    output$foo <- downloadHandler( #Download plotly heatmap
         filename = "dremi_heatmap.pdf",
         content = function(file_origin) {
             if (!is.null(input$in6) & !is.null(input$in12)) {

code/aux/aux5v1_emd.R

@@ -27,7 +27,7 @@ print(minx, maxx)
 ###############################################################################
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#~UI~#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ###############################################################################
-# Define UI for application that draws a histogram
+
 ui <- fluidPage(
 
     # Application title
@@ -61,12 +61,12 @@ ui <- fluidPage(
 ###############################################################################
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#~Server~#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ###############################################################################
-# Define server logic required to draw a histogram
+
 server <- function(input, output, session) {
 
     output$out6 <- renderPrint(input$in6)
 
-    output$trendPlot <- renderPlotly({
+    output$trendPlot <- renderPlotly({ #Process input data and make plotly heatmap
         if (!is.null(input$in6) & !is.null(input$in12)) {
             data_to_plot <- emd_info %>% filter(marker %in% input$in6) %>% filter(file_origin %in% input$in12)
             data_to_plot$file_origin <- as.factor(data_to_plot$file_origin) %>% fct_relevel(input$in12)
@@ -79,7 +79,6 @@ server <- function(input, output, session) {
             data_to_plot$file_origin <- as.factor(data_to_plot$file_origin) %>% fct_relevel(input$in12)
         }
         else{data_to_plot <- emd_info}
-        # saveRDS(data_to_plot, "testdata.RDS")
         initial_emd <- data_to_plot %>% ggplot(aes(x=file_origin, y=fct_rev(marker))) + geom_tile(aes(fill=EMD_no_norm_arc))
         print(
         ggplotly(initial_emd + scale_fill_distiller(
@@ -94,7 +93,7 @@ server <- function(input, output, session) {
             ggtitle("EMD scores heatmap")
         ) %>% layout(height = 700, width = 700))
     })
-    output$complexheatmap <- renderPlot({ ###TESTING ADDITION OF COMPLEXHEATMAP###
+    output$complexheatmap <- renderPlot({ #Process input data and make ComplexHeatmap
         if (!is.null(input$in6) & !is.null(input$in12)) {
             data_to_plot <- emd_info %>% filter(marker %in% input$in6) %>% filter(file_origin %in% input$in12)
             data_to_plot$file_origin <- as.factor(data_to_plot$file_origin) %>% fct_relevel(input$in12)
@@ -114,7 +113,7 @@ server <- function(input, output, session) {
         Heatmap(t(df_mat), name="EMD scores", column_title="Conditions",row_title="Markers",column_names_rot=60)
     }, width=600, height=800)
 
-    output$foo <- downloadHandler(
+    output$foo <- downloadHandler( #Download plotly heatmap
         filename = "emd_heatmap.pdf",
         content = function(file) {
             if (!is.null(input$in6) & !is.null(input$in12)) {
@@ -145,7 +144,7 @@ server <- function(input, output, session) {
             , device = "pdf")
         }
     )
-    output$complex <- downloadHandler(
+    output$complex <- downloadHandler( #Download ComplexHeatmap
         filename = "emd_complexheatmap.pdf",
         content = function(file) {
             if (!is.null(input$in6) & !is.null(input$in12)) {
@@ -179,6 +178,6 @@ if (getOption("browser") == "") {
     options(browser="xdg-open")
     print("R encountered an error when identifying your default browser.")
     print("Please manually open in your browser the addres indicated below.")
-} #The block below solves the utils::browseURL(appUrl) ERROR present in certain conda/WSL installs
+} #The block above solves the utils::browseURL(appUrl) ERROR present in certain conda/WSL installs
 
 shinyApp(ui = ui, server = server) #, options = list(launch.browser=TRUE))