pathway bug fixe

.gitignore

@@ -12,6 +12,7 @@ vignettes/.html
 .renviron
 .rprofile
 .rproj
+.Rproj
 .rproj.user
 .rhistory
 .rapp.history

R/mafCompare.R

@@ -7,8 +7,8 @@
 #' @param m2Name optional name for second cohort
 #' @param minMut Consider only genes with minimum this number of samples mutated in atleast one of the cohort for analysis. Helful to ignore single mutated genes. Default 5.
 #' @param useCNV whether to include copy number events. Default TRUE if available.. Not applicable when `pathways = TRUE`
-#' @param pathways Summarize genes by pathways before comparing. Default `FALSE`
-#' @param custom_pw Optional. Can be a two column data.frame/tsv-file with pathway-name and genes involved in them. Default `NULL`, uses a predefined list of pathways. Applicable only when `pathways = TRUE`
+#' @param pathways Summarize genes by pathways before comparing. Can be either `sigpw` or `smgbp`,  `sigpw` uses known oncogenic signalling pathways (Sanchez/Vega et al) whereas `smgbp` uses pan cancer significantly mutated genes classified according to biological process (Bailey et al). Default \code{NULL}
+#' @param custom_pw Optional. Can be a two column data.frame/tsv-file with pathway-name and genes involved in them. Default `NULL`. This argument is mutually exclusive with \code{pathdb}
 #' @param pseudoCount If TRUE, adds 1 to the contingency table with 0's to avoid `Inf` values in the estimated odds-ratio.
 #' @return result list
 #' @examples
@@ -22,7 +22,7 @@
 #' @seealso \code{\link{forestPlot}}
 #' @seealso \code{\link{lollipopPlot2}}
 
-mafCompare = function(m1, m2, m1Name = NULL, m2Name = NULL, minMut = 5, useCNV = TRUE, pathways = FALSE, custom_pw = NULL, pseudoCount = FALSE){
+mafCompare = function(m1, m2, m1Name = NULL, m2Name = NULL, minMut = 5, useCNV = TRUE, pathways = NULL, custom_pw = NULL, pseudoCount = FALSE){
 
   m1.gs <- getGeneSummary(x = m1)
   m2.gs <- getGeneSummary(x = m2)
@@ -43,13 +43,28 @@ mafCompare = function(m1, m2, m1Name = NULL, m2Name = NULL, minMut = 5, useCNV =
     SampleSize = c(m1.sampleSize, m2.sampleSize)
   )
 
-  if(pathways){
+  if(!is.null(custom_pw)){
+
+    if(is.data.frame(custom_pw)){
+      colnames(custom_pw)[1:2] = c("Pathway", "Gene")
+    } else if(file.exists(custom_pw)){
+      custom_pw = data.table::fread(file = custom_pw)
+      colnames(custom_pw)[1:2] = c("Pathway", "Gene")
+    }
+
     m1_pw = get_pw_summary(maf = m1, pathways = custom_pw)[,.(Pathway, Mutated_samples)]
     m2_pw = get_pw_summary(maf = m2, pathways = custom_pw)[,.(Pathway, Mutated_samples)]
 
     m.gs.meged = merge(m1_pw, m2_pw, by = "Pathway", all = TRUE)
     m.gs.meged = as.data.frame(m.gs.meged)
 
+  }else if(!is.null(pathways)){
+    pw_db = match.arg(arg = pathways, choices = c("sigpw", "smgbp"))
+    m1_pw = get_pw_summary(maf = m1, pathways = pw_db)[,.(Pathway, Mutated_samples)]
+    m2_pw = get_pw_summary(maf = m2, pathways = pw_db)[,.(Pathway, Mutated_samples)]
+
+    m.gs.meged = merge(m1_pw, m2_pw, by = "Pathway", all = TRUE)
+    m.gs.meged = as.data.frame(m.gs.meged)
   }else{
     if(useCNV){
       m1.genes = as.character(m1.gs[AlteredSamples >= minMut,Hugo_Symbol])

R/oncoPathway.R

@@ -12,7 +12,6 @@
 #' @param plotType Can be 'treemap' or 'bar'. Set NA to suppress plotting. Default NA
 #' @param fontSize Default 1
 #' @param panelWidths Default c(2, 4, 4)
-#' @param fontsize Defalt 1
 #' @param col Default #f39c12
 #' @return fraction of altered pathway. attr genes contain pathway contents
 #' @seealso \code{\link{plotPathways}}
@@ -28,10 +27,10 @@ pathways = function(maf, pathdb = "sigpw", pathways = NULL, fontSize = 1, panelW
   if(is.null(pathways)){
     pathways = match.arg(arg = pathdb, choices = c("sigpw", "smgbp"))
   }else{
-    if(file.exists(pathways)){
-      pathways = data.table::fread(file = pathways)
+    if(is.data.frame(pathways)){
       colnames(pathways)[1:2] = c("Pathway", "Gene")
-    }else if(is.data.frame(pathways)){
+    } else if(file.exists(pathways)){
+      pathways = data.table::fread(file = pathways)
       colnames(pathways)[1:2] = c("Pathway", "Gene")
     }
   }

R/oncomatrix.R

@@ -681,7 +681,12 @@ update_colors = function(x, y){
 
 #Get pathway summary from an MAF
 get_pw_summary = function(maf, pathways = NULL){
-  if(pathways %in% c("sigpw", "smgbp")){
+
+  if(is(pathways, class2 = "data.frame")){
+    pathdb = data.table::copy(x = pathways)
+    colnames(pathdb)[1:2] = c("Pathway", "Gene")
+    data.table::setDT(x = pathdb)
+  }else if(pathways %in% c("sigpw", "smgbp")){
     if(pathways == "sigpw"){
       pathdb <- system.file("extdata", "oncogenic_sig_patwhays.tsv", package = "maftools")
       message("Summarizing signalling pathways [Sanchez-Vega et al., https://doi.org/10.1016/j.cell.2018.03.035]")
@@ -691,11 +696,9 @@ get_pw_summary = function(maf, pathways = NULL){
     }
     pathdb = data.table::fread(file = pathdb)
     colnames(pathdb)[1:2] = c("Pathway", "Gene")
-  }else{
-    pathdb = data.table::copy(x = pathways)
-    colnames(pathdb)[1:2] = c("Pathway", "Gene")
-    data.table::setDT(x = pathdb)
   }
+
+
   pathdb_size = pathdb[,.N,Pathway]
   pathdb = split(pathdb, as.factor(pathdb$Pathway))
 

R/plotPathways.R

@@ -1,20 +1,3 @@
-#' Plot oncogenic pathways
-#' @references Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S et al. 2018. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173: 321-337 e310
-#'
-#' @details
-#' Draws oncoplot of oncogenic pathway.
-#' @param maf an \code{\link{MAF}} object generated by \code{\link{read.maf}}
-#' @param pathways Name of pathways to be drawn
-#' @param pathdb A tsv file or a data frame containing pathway to gene mappings. If not provided uses the default resource. Data must contain at least two columns with pathway name and gene names. Optionally a third column with OG or TSG information can be added.
-#' @param fullPathway Include all genes from the pathway. Defaulr FALS only plots mutated genes
-#' @param removeNonMutated Default TRUE
-#' @param tsgCol Color for tumro suppressor genes. Default red
-#' @param ogCol Color for onco genes. Default royalblue
-#' @param fontSize Default 0.6
-#' @param showTumorSampleBarcodes logical to include sample names.
-#' @param SampleNamefontSize font size for sample names. Default 10
-#' @param sampleOrder Manually speify sample names for oncolplot ordering. Default NULL.
-
 plotPathways = function(maf, pathways = NULL, fullPathway = FALSE, pathdb = NULL,
                                  removeNonMutated = TRUE, tsgCol = "red", ogCol = "royalblue", fontSize = 0.6, showTumorSampleBarcodes = FALSE, sampleOrder = NULL, SampleNamefontSize = 0.6){
 

inst/NEWS.md

@@ -7,6 +7,7 @@
 - `readGistic` can take gistic output directory as an input. PR by [biosunsci](https://github.com/biosunsci) [954](https://github.com/PoisonAlien/maftools/pull/954)
 
 ## BUG FIXES
+- Bug fixes while processing custom pathways
 - Bug fix in `oncoplot` for drawing borders. [958](https://github.com/PoisonAlien/maftools/issues/958)
 - Bug fix in `plotSignatures` for hardcoded axis limits. [949](https://github.com/PoisonAlien/maftools/issues/949)
 - Bug fix in `mafSurvival` legend when samples argument is give. [937](https://github.com/PoisonAlien/maftools/issues/937)