Added GOI table printing for Filtering

NIDAP-Community · Aug 1, 2023 · 2a7be1a · 2a7be1a
1 parent 0abf579
commit 2a7be1a
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Showing 6 changed files with 9 additions and 3 deletions.
diff --git a/R/filtering.R b/R/filtering.R
@@ -154,9 +154,10 @@ filtering <- function(object, loq.cutoff, loq.min, cut.segment, goi) {
   if(class(goi)[1] != "character"){
     stop(paste0("Error: You have the wrong data class, must be character vector" ))
   }
-  goi.df <- data.frame(Gene = goi,
+  goi.table <- data.frame(Gene = goi,
                        Number = fData(object)[goi, "DetectedSegments"],
                        DetectionRate = percent(fData(object)[goi, "DetectionRate"]))
+  #goi.table <- capture.output(print(goi.df, row.name = FALSE))
 
   ## 4.5.3 Gene Filtering
   # Plot detection rate:
@@ -191,5 +192,5 @@ filtering <- function(object, loq.cutoff, loq.min, cut.segment, goi) {
   # retain only detected genes of interest
   goi <- goi[goi %in% rownames(object)]
 
-  return(list("stacked.bar.plot" = stacked.bar.plot, "tab" = tab, "sankey.plot" = sankey.plot, "genes.detected.plot" = genes.detected.plot, "object" = object))
+  return(list("stacked.bar.plot" = stacked.bar.plot, "tab" = tab, "sankey.plot" = sankey.plot, "goi.table" = goi.table, "genes.detected.plot" = genes.detected.plot, "object" = object))
 }
diff --git a/vignettes/Integration_Test_CPTR_Colon.Rmd b/vignettes/Integration_Test_CPTR_Colon.Rmd
@@ -71,7 +71,7 @@ This runs the DSPworkflow package to completion using the Human Colon Cancer Dat
   
   print(sdesign.list$sankey.plot)
   print("Created GeoMx Object\n\n")
-  pData(sdesign.list$object)[,c("slide name","class","segment")]  
+  pData(sdesign.list$object)[,c("slide_name","class","segment")]  
   
   
 ```
@@ -117,6 +117,7 @@ qc.output <-  qcProc(object = sdesign.list$object,
     print(filtering.output$`tab`)
     print(filtering.output$`sankey.plot`)
     print(filtering.output$`genes.detected.plot`)
+    print(filtering.output$'goi.table', row.names = FALSE)
     
   create.rds <- FALSE
   if(create.rds) {

diff --git a/vignettes/Integration_Test_Colon.Rmd b/vignettes/Integration_Test_Colon.Rmd
@@ -123,6 +123,7 @@ This runs the DSPworkflow package to completion using the Human Colon Dataset:
     print(filtering.output$`tab`)
     print(filtering.output$`sankey.plot`)
     print(filtering.output$`genes.detected.plot`)
+    print(filtering.output$'goi.table', row.names = FALSE)
     
   create.rds <- TRUE
   if(create.rds) {

diff --git a/vignettes/Integration_Test_Kidney.Rmd b/vignettes/Integration_Test_Kidney.Rmd
@@ -125,6 +125,7 @@ qc.output <-  qcProc(object = sdesign.list$object,
     print(filtering.output$`tab`)
     print(filtering.output$`sankey.plot`)
     print(filtering.output$`genes.detected.plot`)
+    print(filtering.output$'goi.table', row.names = FALSE)
     
   create.rds <- TRUE
   if(create.rds) {

diff --git a/vignettes/Integration_Test_Mouse_Thymus.Rmd b/vignettes/Integration_Test_Mouse_Thymus.Rmd
@@ -124,6 +124,7 @@ qc.output <-  qcProc(object = sdesign.list$object,
     print(filtering.output$`tab`)
     print(filtering.output$`sankey.plot`)
     print(filtering.output$`genes.detected.plot`)
+    print(filtering.output$'goi.table', row.names = FALSE)
     
   create.rds <- TRUE
   if(create.rds) {

diff --git a/vignettes/Integration_Test_NSCLC.Rmd b/vignettes/Integration_Test_NSCLC.Rmd
@@ -128,6 +128,7 @@ qc.output <-  qcProc(object = sdesign.list$object,
     print(filtering.output$`tab`)
     print(filtering.output$`sankey.plot`)
     print(filtering.output$`genes.detected.plot`)
+    print(filtering.output$'goi.table', row.names = FALSE)
     
   create.rds <- TRUE
   if(create.rds) {