AlexsLemonade · jaclyn-taroni · May 13, 2021 · Apr 29, 2021 · Apr 29, 2021 · May 3, 2021
diff --git a/analyses/oncoprint-landscape/01-plot-oncoprint.R b/analyses/oncoprint-landscape/01-plot-oncoprint.R
@@ -95,6 +95,12 @@ option_list <- list(
     default = NULL,
     help = "optional name of `broad_histology` value to plot associated oncoprint"
   ),
+  optparse::make_option(
+    c("-n", "--top_n"),
+    type = "integer",
+    default = NULL,
+    help = "optional `n` to display top n genes based on count of mutations"
+  ),
   optparse::make_option(
     c("-p", "--png_name"),
     type = "character",
@@ -115,22 +121,6 @@ cnv_df <- opt$cnv_file
 fusion_df <- opt$fusion_file
 goi_list <- opt$goi_list
 
-#### Functions ----------------------------------------------------------------
-
-read_genes <- function(gene_list) {
-  # This function takes in the file path to a gene list and pulls out
-  # the gene information from that list
-  #
-  # Args:
-  #   gene_list: file path to genes of interest file
-  #
-  # Return:
-  #   genes: a vector of genes from the genes of interest file
-
-  genes <- readr::read_tsv(gene_list) %>%
-    dplyr::pull("gene")
-}
-
 #### Read in data --------------------------------------------------------------
 
 # Read in metadata
@@ -154,12 +144,10 @@ if (!is.null(opt$fusion_file)) {
 
 # Read in gene information from the list of genes of interest files
 if (!is.null(opt$goi_list)) {
-  goi_files <- unlist(stringr::str_split(goi_list, ",| "))
-  # Read in using the `read_genes` custom function and unlist the gene column
-  # data from the genes of interest file paths given
-  goi_list <- lapply(goi_files, read_genes)
-    # Include only the unique genes of interest
-  goi_list <- unique(unlist(goi_list))
+  # Read in using the `read_tsv()` function
+  goi_list <- readr::read_tsv(tolower(gsub(" ", "-",opt$goi_list))) %>%
+    as.matrix()
+
 }
 
 #### Set up oncoprint annotation objects --------------------------------------
@@ -251,6 +239,37 @@ maf_object <- prepare_maf_object(
   fusion_df = fusion_df
 )
 
+#### Subset MAF Object (Optional)----------------------------------------------
+
+# Code here is specifically adapted from:
+# https://github.com/marislab/create-pptc-pdx-oncoprints/blob/master/R/create-complexheat-oncoprint-revision.R
+
+# Subset `maf_object` for histology-specific goi list
+if (!is.null(opt$goi_list)) {
+  maf_object = subsetMaf(
+    maf = maf_object,
+    tsb = metadata$Tumor_Sample_Barcode,
+    genes = goi_list,
+    mafObj = TRUE
+  )
+
+  # Get top mutated genes per this subset object
+  gene_sum <- mafSummary(maf_object)$gene.summary
+
+  # Sort to get top altered genes rather than mutated only genes
+  goi_ordered <-
+    gene_sum[order(gene_sum$AlteredSamples, decreasing = T),]
+
+  if (!is.null(opt$top_n)) {
+
+    # Select top `n` genes if the argument is provided
+    top_n <- ifelse(nrow(gene_sum) < opt$top_n, nrow(gene_sum), opt$top_n)
+
+    goi_list <- goi_ordered[1:top_n,]
+
+  }
+
+}
-# Subset `maf_object` for histology-specific goi list
-if (!is.null(opt$goi_list)) {
-  maf_object = subsetMaf(
-    maf = maf_object,
-    tsb = metadata$Tumor_Sample_Barcode,
-    genes = goi_list,
-    mafObj = TRUE
-  )
-  
-  # Get top mutated genes per this subset object
-  gene_sum <- mafSummary(maf_object)$gene.summary
-  
-  # Sort to get top altered genes rather than mutated only genes
-  goi_ordered <-
-    gene_sum[order(gene_sum$AlteredSamples, decreasing = T),]
-  
-  if (!is.null(opt$top_n)) {
-    
-    # Select top `n` genes if the argument is provided
-    top_n <- ifelse(nrow(gene_sum) < opt$top_n, nrow(gene_sum), opt$top_n)
-    
-    goi_list <- goi_ordered[1:top_n,]
-    
-  }
-  
-}
+# Subset `maf_object` for histology-specific goi list
+if (!is.null(opt$goi_list) & !is.null(opt$top_n)) {
+  
+  maf_object <- subsetMaf(
+    maf = maf_object,
+    tsb = metadata$Tumor_Sample_Barcode,
+    genes = goi_list,
+    mafObj = TRUE
+  )
+  
+  # Get top mutated genes per this subset object
+  gene_sum <- mafSummary(maf_object)$gene.summary
+  
+  # Sort to get top altered genes rather than mutated only genes
+  goi_ordered <-
+    gene_sum[order(gene_sum$AlteredSamples, decreasing = T),]
+  
+  # Select top `n` genes if the argument is provided
+  top_n <- ifelse(nrow(gene_sum) < opt$top_n, nrow(gene_sum), opt$top_n)
+  goi_list <- goi_ordered[1:top_n,]
+  
+}
-# Subset `maf_object` for histology-specific goi list
-if (!is.null(opt$goi_list)) {
-  maf_object = subsetMaf(
-    maf = maf_object,
-    tsb = metadata$Tumor_Sample_Barcode,
-    genes = goi_list,
-    mafObj = TRUE
-  )
-  
-  # Get top mutated genes per this subset object
-  gene_sum <- mafSummary(maf_object)$gene.summary
-  
-  # Sort to get top altered genes rather than mutated only genes
-  goi_ordered <-
-    gene_sum[order(gene_sum$AlteredSamples, decreasing = T),]
-  
-  if (!is.null(opt$top_n)) {
-    
-    # Select top `n` genes if the argument is provided
-    top_n <- ifelse(nrow(gene_sum) < opt$top_n, nrow(gene_sum), opt$top_n)
-    
-    goi_list <- goi_ordered[1:top_n,]
-    
-  }
-  
-}
+# Subset `maf_object` for histology-specific goi list
+if (!is.null(opt$goi_list) & !is.null(opt$top_n)) {
+  
+  maf_object <- subsetMaf(
+    maf = maf_object,
+    tsb = metadata$Tumor_Sample_Barcode,
+    genes = goi_list,
+    mafObj = TRUE
+  )
+  
+  # Get top mutated genes per this subset object
+  gene_sum <- mafSummary(maf_object)$gene.summary
+  
+  # Sort to get top altered genes rather than mutated only genes
+  goi_ordered <-
+    gene_sum[order(gene_sum$AlteredSamples, decreasing = T),]
+  
+  # Select top `n` genes if the argument is provided
+  top_n <- ifelse(nrow(gene_sum) < opt$top_n, nrow(gene_sum), opt$top_n)
+  goi_list <- goi_ordered[1:top_n,]
+  
+}
 #### Plot and Save Oncoprint --------------------------------------------------
 
 # Given a maf object, plot an oncoprint of the variants in the
@@ -265,7 +284,7 @@ png(
 oncoplot(
   maf_object,
   clinicalFeatures = "display_group",
-  genes = goi_list,
+  genes = goi_list$Hugo_Symbol,
   logColBar = TRUE,
   sortByAnnotation = TRUE,
   showTumorSampleBarcodes = TRUE,
@@ -279,3 +298,4 @@ oncoplot(
   top = 25
 )
 dev.off()
+
diff --git a/analyses/oncoprint-landscape/data/diffuse-astrocytic-and-oligodendroglial-tumor_goi_list.tsv b/analyses/oncoprint-landscape/data/diffuse-astrocytic-and-oligodendroglial-tumor_goi_list.tsv
@@ -0,0 +1,82 @@
+HGAT
+H3F3A
+TP53
+ATRX
+PPM1D
+PIK3CA
+NF1
+PIK3R1
+PDGFRA
+ACVR1
+PTEN
+EGFR
+ATM
+FGFR1
+CCND2
+HIST1H3B
+KIT
+KDR
+CDKN2A
+MET
+IGF1R
+BRAF
+IDH1
+MYCN
+CDK4
+ID2
+MYC
+TOP3A
+CDK6
+ASXL1
+KRAS
+MDM2
+TERT
+MAFK
+PDGFA
+PIK3C2B
+PLAGL2
+GAB2
+AURKB
+NFIB
+PIK3C2G
+AKT1
+CCND1
+ID3
+APOBEC3H
+AKT2
+GOLPH3
+FGFR2
+BCOR
+CDKN1B
+CDKN1C
+RB1
+SMARCE1
+CDKN2C
+CIC
+DIS3L2P1
+CDKN2B
+SETD2
+KDM6B
+NTRK1
+NTRK2
+NTRK3
+HIST1H3C
+HIST2H3C
+DDX11
+TSC2
+DDR2
+TOP2A
+FOSB
+VEGFA
+NRAS
+MTOR
+PTPN11
+FANCA
+SLCO1B3
+PDGFC
+YES1
+FYN
+POLE
+HIST1H2BE
+KMT2C
+TDRD9
diff --git a/analyses/oncoprint-landscape/data/embryonal-tumor_goi_list.tsv b/analyses/oncoprint-landscape/data/embryonal-tumor_goi_list.tsv
@@ -0,0 +1,63 @@
+Embryonal tumor
+DICER1
+TP53
+MSH2
+TERT
+TFPT
+PAARP8
+CENPE
+DDX11
+MUTYH
+CHEK2
+CTNNB1
+DYNC2H1
+PTCH1
+MAP4K4
+SUFU
+ROS1
+KSR2
+RASSF5
+FOXO3
+IGFN1
+BCOR
+TTYH1
+MIR17HG
+LIN28A
+APC
+CSNK2B
+SMO
+KMT2D
+SMARCA4
+PRDM6
+KMT2C
+KDM6A
+CREBBP
+ZMYM3
+GSE1
+ARID1A
+MED12
+GFIB
+MYCN
+OTX2
+TCF4
+ZIC1
+GFI1
+TBR1
+BRCA2
+ATM
+PTEN
+PIK3CA
+PRKAR1A
+BAI3
+EPHA7
+KBTBD4
+CTDNEP1
+DDX3X
+SYNCRIP
+IDH1
+CDK6
+SNCAIP
+FOXR2
+BEND2
+MN1
+SMARCB1
diff --git a/analyses/oncoprint-landscape/data/ependymal-tumor_goi_list.tsv b/analyses/oncoprint-landscape/data/ependymal-tumor_goi_list.tsv
@@ -0,0 +1,14 @@
+Ependymal tumor
+H3F3A
+CDKN2A
+RELA
+YAP1
+C11orf95
+MAMLD1
+FAM118B
+MAML2
+NF2
+CLDN1
+PTEN
+ARL4D
+L1CAM
diff --git a/analyses/oncoprint-landscape/data/low-grade-astrocytic-tumor_goi_list.tsv b/analyses/oncoprint-landscape/data/low-grade-astrocytic-tumor_goi_list.tsv
@@ -0,0 +1,28 @@
+LGAT
+KIAA1549
+BRAF
+FGFR1
+TACC1
+MYB
+MYBL
+NTRK1
+NTRK2
+NTRK3
+IDH
+H3F3A
+RAF1
+PTPN11
+TSC1
+TSC2
+PIK3CA
+PRKCA
+FGFR2
+FGFR3
+MAP2K1
+ALK
+ROS1
+QKI
+KRAS
+TP53
+ATRX
+CDKN2A
diff --git a/analyses/oncoprint-landscape/data/oncoprint-goi-lists-OpenPBTA.csv b/analyses/oncoprint-landscape/data/oncoprint-goi-lists-OpenPBTA.csv
@@ -0,0 +1,82 @@
+LGAT,Source,Embryonal tumor,Source,HGAT,Source,Ependymal tumor,Source,Other,Source
+KIAA1549,RYALL 2020,DICER1,LAMBO 2020,H3F3A,MACKAY 2017,H3F3A,RYALL 2017,CTNNB1,SEKINE 2002
+BRAF,RYALL 2020,TP53,LAMBO 2020,TP53,MACKAY 2017,CDKN2A,PAJTLER 2015,BRAF,QADDOUMI 2016
+FGFR1,RYALL 2020,MSH2,LAMBO 2020,ATRX,MACKAY 2017,RELA,PAJTLER 2015,FGFR1,QADDOUMI 2016
+TACC1,RYALL 2020,TERT,LAMBO 2020,PPM1D,MACKAY 2017,YAP1,PAJTLER 2015,MYB,QADDOUMI 2016
+MYB,RYALL 2020,TFPT,LAMBO 2020,PIK3CA,MACKAY 2017,C11orf95,PAJTLER 2015,KRAS,QADDOUMI 2016
+MYBL,RYALL 2020,PAARP8,LAMBO 2020,NF1,MACKAY 2017,MAMLD1,PAJTLER 2015,IDH1,QADDOUMI 2016
+NTRK1,RYALL 2020,CENPE,LAMBO 2020,PIK3R1,MACKAY 2017,FAM118B,PAJTLER 2015,IDH2,QADDOUMI 2016
+NTRK2,RYALL 2020,DDX11,LAMBO 2020,PDGFRA,MACKAY 2017,MAML2,PAJTLER 2015,H3F3A,QADDOUMI 2016
+NTRK3,RYALL 2020,MUTYH,LAMBO 2020,ACVR1,MACKAY 2017,NF2,PAJTLER 2015,FGFR3,QADDOUMI 2016
+IDH,RYALL 2020,CHEK2,LAMBO 2020,PTEN,MACKAY 2017,CLDN1,PAJTLER 2015,PDGFRA,QADDOUMI 2016
+H3F3A,RYALL 2020,CTNNB1,LAMBO 2020,EGFR,MACKAY 2017,PTEN,PAJTLER 2015,NTRK2,QADDOUMI 2016
+RAF1,RYALL 2020,DYNC2H1,LAMBO 2020,ATM,MACKAY 2017,ARL4D,PAJTLER 2015,MYBL1,QADDOUMI 2016
+PTPN11,RYALL 2020,PTCH1,LAMBO 2020,FGFR1,MACKAY 2017,L1CAM,PARKER 2014,TACC1,QADDOUMI 2016
+TSC1,RYALL 2020,MAP4K4,LAMBO 2020,CCND2,MACKAY 2017,,,MAML2,QADDOUMI 2016
+TSC2,RYALL 2020,SUFU,LAMBO 2020,HIST1H3B,MACKAY 2017,,,QKI,QADDOUMI 2016
+PIK3CA,RYALL 2020,ROS1,LAMBO 2020,KIT,MACKAY 2017,,,PATZ1,QADDOUMI 2016
+PRKCA,RYALL 2020,KSR2,LAMBO 2020,KDR,MACKAY 2017,,,EGFR,QADDOUMI 2016
+FGFR2,RYALL 2020,RASSF5,LAMBO 2020,CDKN2A,MACKAY 2017,,,EWSR1,QADDOUMI 2016
+FGFR3,RYALL 2020,FOXO3,LAMBO 2020,MET,MACKAY 2017,,,NF2,BI 2017
+MAP2K1,RYALL 2020,IGFN1,LAMBO 2020,IGF1R,MACKAY 2017,,,SMARCB1,BI 2017
+ALK,RYALL 2020,BCOR,LAMBO 2020,BRAF,MACKAY 2017,,,AKT1,BI 2017
+ROS1,RYALL 2020,TTYH1,LAMBO 2020,IDH1,MACKAY 2017,,,AKT3,BI 2017
+QKI,RYALL 2020,MIR17HG,LAMBO 2020,MYCN,MACKAY 2017,,,PIK3CA,BI 2017
+KRAS,RYALL 2020,LIN28A,LAMBO 2020,CDK4,MACKAY 2017,,,SMP,BI 2017
+TP53,RYALL 2020,CTNNB1,NORTHCOTT 2017,ID2,MACKAY 2017,,,SUFU,BI 2017
+ATRX,RYALL 2020,APC,NORTHCOTT 2017,MYC,MACKAY 2017,,,POLRA2,BI 2017
+CDKN2A,RYALL 2020,CSNK2B,NORTHCOTT 2017,TOP3A,MACKAY 2017,,,BAP1,BI 2017
+,,PTCH1,NORTHCOTT 2017,CDK6,MACKAY 2017,,,TERT,BI 2017
+,,SUFU,NORTHCOTT 2017,ASXL1,MACKAY 2017,,,KLF4,YOUNGBLOOD 2019
+,,SMO,NORTHCOTT 2017,KRAS,MACKAY 2017,,,TP53,YOUNGBLOOD 2019
+,,KMT2D,NORTHCOTT 2017,MDM2,MACKAY 2017,,,LYST,YOUNGBLOOD 2019
+,,SMARCA4,NORTHCOTT 2017,TERT,MACKAY 2017,,,CDKN2A,YOUNGBLOOD 2019
+,,PRDM6,NORTHCOTT 2017,MAFK,MACKAY 2017,,,PIK3CA,YOUNGBLOOD 2019
+,,KMT2C,NORTHCOTT 2017,PDGFA,MACKAY 2017,,,PTEN,YOUNGBLOOD 2019
+,,KDM6A,NORTHCOTT 2017,PIK3C2B,MACKAY 2017,,,PIK3R1,YOUNGBLOOD 2019
+,,CREBBP,NORTHCOTT 2017,PLAGL2,MACKAY 2017,,,PBRM1,YOUNGBLOOD 2019
+,,ZMYM3,NORTHCOTT 2017,GAB2,MACKAY 2017,,,SETD2,YOUNGBLOOD 2019
+,,GSE1,NORTHCOTT 2017,AURKB,MACKAY 2017,,,ARID1A,YOUNGBLOOD 2019
+,,BCOR,NORTHCOTT 2017,NFIB,MACKAY 2017,,,TERT,YOUNGBLOOD 2019
+,,ARID1A,NORTHCOTT 2017,PIK3C2G,MACKAY 2017,,,SMAD4,YOUNGBLOOD 2019
+,,MED12,NORTHCOTT 2017,AKT1,MACKAY 2017,,,SDHA,YOUNGBLOOD 2019
+,,ARID1A,NORTHCOTT 2017,CCND1,MACKAY 2017,,,DDB2,YOUNGBLOOD 2019
+,,GFIB,NORTHCOTT 2017,ID3,MACKAY 2017,,,PRPRD,YOUNGBLOOD 2019
+,,MYCN,NORTHCOTT 2017,APOBEC3H,MACKAY 2017,,,CDC27,YOUNGBLOOD 2019
+,,MYCN,NORTHCOTT 2017,AKT2,MACKAY 2017,,,ARHGAP26,YOUNGBLOOD 2019
+,,OTX2,NORTHCOTT 2017,GOLPH3,MACKAY 2017,,,ERBB4,YOUNGBLOOD 2019
+,,TCF4,NORTHCOTT 2017,FGFR2,MACKAY 2017,,,BLM,YOUNGBLOOD 2019
+,,ZIC1,NORTHCOTT 2017,BCOR,MACKAY 2017,,,USP9X,YOUNGBLOOD 2019
+,,GFI1,NORTHCOTT 2017,CDKN1B,MACKAY 2017,,,TERT,THOMAS 2020
+,,TBR1,NORTHCOTT 2017,CDKN1C,MACKAY 2017,,,PRKCA,THOMAS 2020
+,,TERT,NORTHCOTT 2017,RB1,MACKAY 2017,,,TP53,THOMAS 2020
+,,TP53,NORTHCOTT 2017,SMARCE1,MACKAY 2017,,,CCDC47,THOMAS 2020
+,,BRCA2,NORTHCOTT 2017,CDKN2C,MACKAY 2017,,,BRAF,KROOKS 2018
+,,ATM,NORTHCOTT 2017,CIC,MACKAY 2017,,,,
+,,PTEN,NORTHCOTT 2017,DIS3L2P1,MACKAY 2017,,,,
+,,PIK3CA,NORTHCOTT 2017,CDKN2B,MACKAY 2017,,,,
+,,PRKAR1A,NORTHCOTT 2017,SETD2,MACKAY 2017,,,,
+,,BAI3,NORTHCOTT 2017,KDM6B,MACKAY 2017,,,,
+,,EPHA7,NORTHCOTT 2017,NTRK1,MACKAY 2017,,,,
+,,KBTBD4,NORTHCOTT 2017,NTRK2,MACKAY 2017,,,,
+,,CTDNEP1,NORTHCOTT 2017,NTRK3,MACKAY 2017,,,,
+,,DDX3X,NORTHCOTT 2017,HIST1H3C,MACKAY 2017,,,,
+,,SYNCRIP,NORTHCOTT 2017,HIST2H3C,MACKAY 2017,,,,
+,,IDH1,NORTHCOTT 2017,DDX11,MUELLER 2019,,,,
+,,CDK6,NORTHCOTT 2017,TSC2,MUELLER 2019,,,,
+,,SNCAIP,NORTHCOTT 2017,DDR2,MUELLER 2019,,,,
+,,FOXR2,LASTOWSKA 2020,TOP2A,MUELLER 2019,,,,
+,,BCOR,LASTOWSKA 2020,FOSB,MUELLER 2019,,,,
+,,BEND2,LASTOWSKA 2020,VEGFA,MUELLER 2019,,,,
+,,MN1,LASTOWSKA 2020,NRAS,PNOC003 MANUSCRIPT 2021,,,,
+,,SMARCB1,,MTOR,PNOC003 MANUSCRIPT 2021,,,,
+,,SMARCA4,,PTPN11,PNOC003 MANUSCRIPT 2021,,,,
+,,,,FANCA,PNOC003 MANUSCRIPT 2021,,,,
+,,,,SLCO1B3,PNOC003 MANUSCRIPT 2021,,,,
+,,,,PDGFC,PNOC003 MANUSCRIPT 2021,,,,
+,,,,YES1,PNOC003 MANUSCRIPT 2021,,,,
+,,,,FYN,PNOC003 MANUSCRIPT 2021,,,,
+,,,,POLE,PNOC003 MANUSCRIPT 2021,,,,
+,,,,HIST1H2BE,PNOC003 MANUSCRIPT 2021,,,,
+,,,,KMT2C,PNOC003 MANUSCRIPT 2021,,,,
+,,,,TDRD9,PNOC003 MANUSCRIPT 2021,,,,