From d15ca709c3f7a476105920a44f374498920ce1ca Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Sat, 29 Jun 2024 18:17:43 -0700
Subject: [PATCH] Remove panel overlap charts

---
 templates/dashboardTemplate.Rmd | 68 ---------------------------------
 1 file changed, 68 deletions(-)

diff --git a/templates/dashboardTemplate.Rmd b/templates/dashboardTemplate.Rmd
index bb984c21..fc2c36e3 100644
--- a/templates/dashboardTemplate.Rmd
+++ b/templates/dashboardTemplate.Rmd
@@ -697,74 +697,6 @@ 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.