[GEN-1326] Remove panel overlap charts (#570)

* Remove panel overlap charts

* Remove unused function

* remove upset

* Remove upsetR

R/install_packages.R

@@ -3,7 +3,6 @@ renv::restore()
 library(synapser)
 library(dplyr)
 library(argparse)
-library(UpSetR)
 library(rmarkdown)
 library(testthat)
 library(VariantAnnotation)

templates/dashboardTemplate.Rmd

@@ -25,7 +25,6 @@ title: '`r release`'
 suppressMessages(library(synapser))
 foo = capture.output(synLogin())
 suppressMessages(library(ggplot2))
-suppressMessages(library(UpSetR))
 suppressMessages(library(RColorBrewer))
 suppressMessages(library(jsonlite))
 suppressMessages(library(knitr))
@@ -57,19 +56,6 @@ getFileDf <- function(fileName, releaseFiles) {
   }
 }
 
-makePanelList = function(assay, bed) {
-  return(unique(as.character(bed$Hugo_Symbol[bed$SEQ_PIPELINE_ID == assay])))
-}
-
-plotPanelOverlap <- function(bed, assays) {
-  listInput = lapply(as.list(assays), function(x) { makePanelList(x, bed) })
-  names(listInput) = assays
-  upset(fromList(listInput),
-        order.by = "freq",
-        nsets = length(assays),
-        nintersects = 30)
-}
-
 plotCenterXRace <- function(genieClinData) {
   t = as.data.frame.matrix(table(genieClinData$CENTER,genieClinData$PRIMARY_RACE))
   t = data.frame(n = rowSums(t),t)
@@ -672,74 +658,6 @@ if (!is.null(assay_infodf) & !is.null(this_bed)) {
 
 ---
 
-## Gene Panel Overlaps
-This section will show the number of genes that overlap between the myeloid, small and large GENIE panels.
-
-```{r bed_process, include=F}
-if (!is.null(this_bed)) {
-  this_bed <- this_bed[this_bed$Feature_Type == "exon",]
-  #Make it so that I use include in panel
-  if (!is.null(this_bed$includeInPanel)) {
-    this_bed <- this_bed[this_bed$includeInPanel == "True",]
-  }
-  noneExistentAssays = this_assays[!this_assays %in% this_bed$SEQ_ASSAY_ID]
-  if (length(noneExistentAssays) > 0) {
-    print(paste("These assays do not have bed files associated with them: ",
-                paste(noneExistentAssays, collapse = ", ")))
-  }
-  this_assays = this_assays[this_assays %in% this_bed$SEQ_ASSAY_ID]
-  myeloid_panels = c("VICC-01-MYELOID","UHN-54-V1","UCHI-ONCOHEME55-V1","CHOP-HEMEP","MSK-IMPACT-HEME-399")
-  myeloid = this_assays[this_assays %in% myeloid_panels]
-
-  normal = this_assays[!this_assays %in% myeloid_panels]
-  seq_pipeline_ids = unique(
-    this_bed$SEQ_PIPELINE_ID[this_bed$SEQ_ASSAY_ID %in% normal]
-  )
-  smallPanels = c()
-  largePanels = c()
-  for (panel in seq_pipeline_ids) {
-    panelDf = this_bed[this_bed$SEQ_PIPELINE_ID == panel,]
-    if (length(table(panelDf$Hugo_Symbol)) < 100) {
-      smallPanels = c(smallPanels, panel)
-      # Don't add to panel if more than 1500 genes
-    } else if (length(table(panelDf$Hugo_Symbol)) < 1500) {
-      largePanels = c(largePanels, panel)
-    }
-  }
-} else {
-  largePanels = c()
-  smallPanels = c()
-  myeloid = c()
-}
-```
-
-### Meyloid Gene Panels
-
-```{r myeloid_panel_upset}
-if (length(myeloid) > 1) {
-  plotPanelOverlap(this_bed, myeloid)
-}
-
-```
-
-### Small (<100) Gene panels
-
-```{r small_panel_upset, fig.height=12}
-if (length(smallPanels) > 1) {
-  plotPanelOverlap(this_bed, smallPanels)
-}
-```
-
-### Large ($\geq$ 100) Gene panels
-
-```{r large_panel_upset, fig.height=12}
-if (length(largePanels) > 1) {
-  plotPanelOverlap(this_bed, largePanels)
-}
-```
-
----
-
 ## Possible Non-center Related Data Issues
 
 This section includes QC issues that are mostly related to the Sage Bionetworks pipeline, Genome Nexus or _maybe_ center related issues.