Adding option to have different x.cuts in volcano

R/TCGAPrepare.R

@@ -639,12 +639,20 @@ get.GRCh.bioMart <- function(genome="hg19") {
                         "ensembl_gene_id",
                         "external_gene_name")
     }
-    message(paste0("Downloading genome information. Using: ",
-                   listDatasets(ensembl)[listDatasets(ensembl)$dataset=="hsapiens_gene_ensembl",]$description))
-    chrom <- c(1:22, "X", "Y")
-    gene.location <- getBM(attributes = attributes,
-                           filters = c("chromosome_name"),
-                           values = list(chrom), mart = ensembl)
+    description <- listDatasets(ensembl)[listDatasets(ensembl)$dataset=="hsapiens_gene_ensembl",]$description
+    message(paste0("Downloading genome information. Using: ", description))
+
+    filename <-  paste0(gsub("[[:punct:]]| ", "_",description),".rda")
+    if(!file.exists(filename)) {
+        chrom <- c(1:22, "X", "Y")
+        gene.location <- getBM(attributes = attributes,
+                               filters = c("chromosome_name"),
+                               values = list(chrom), mart = ensembl)
+        save(gene.location, file = filename)
+    } else {
+        message("Loading")
+        gene.location <- get(load(filename))
+    }
 
     return(gene.location)
 }

R/TCGAvisualize.R

@@ -926,7 +926,7 @@ unlistlabels <- function(lab) {
 #' @importFrom grid gpar grid.rect
 #' @importFrom data.table dcast setDT setDF :=
 #' @examples
-#' mut <- GDCquery_Maf(tumor = "ACC", pipelines = "muse")
+#' mut <- GDCquery_Maf(tumor = "ACC", pipelines = "mutect")
 #' TCGAvisualize_oncoprint(mut = mut, genes = mut$Hugo_Symbol[1:10], rm.empty.columns = TRUE)
 #' TCGAvisualize_oncoprint(mut = mut, genes = mut$Hugo_Symbol[1:10],
 #'                  filename = "onco.pdf",
@@ -1050,8 +1050,11 @@ TCGAvisualize_oncoprint <- function (mut,
 
     if(missing(annotation)) annotation <- NULL
     if(!is.null(annotation)){
+        if(!"bcr_patient_barcode" %in% colnames(annotation))
+            stop("bcr_patient_barcode column should be in the annotation")
         idx <- match(substr(colnames(mat),1,12),annotation$bcr_patient_barcode)
-
+        if(all(is.na(idx)))
+            stop(" We couldn't match the columns names with the bcr_patient_barcode column in the annotation object")
         annotation <- annotation[idx,]
 
         annotation$bcr_patient_barcode <- NULL

R/methylation.R

@@ -659,8 +659,9 @@ calculate.pvalues <- function(data,
 #'    Observation: This function automatically is called by TCGAanalyse_DMR
 #' @param x x-axis data
 #' @param y y-axis data
-#' @param y.cut p-values threshold. Default: 0.01
-#' @param x.cut  x-axis threshold. Default: 0.0
+#' @param y.cut p-values threshold.
+#' @param x.cut  x-axis threshold. Default: 0.0 If you give only one number (e.g. 0.2) the cut-offs will be
+#'  -0.2 and 0.2. Or you can give diffenrent cutt-ofs as a vector (e.g. c(-0.3,0.4))
 #' @param filename Filename. Default: volcano.pdf, volcano.svg, volcano.png
 #' @param legend Legend title
 #' @param color vector of colors to be used in graph
@@ -696,6 +697,9 @@ calculate.pvalues <- function(data,
 #' TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=0.8,
 #'                       names = as.character(1:length(x)), legend = "Status",
 #'                       names.fill = TRUE, highlight = c("1","2"),show="both")
+#' TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=c(-0.3,0.8),
+#'                       names = as.character(1:length(x)), legend = "Status",
+#'                       names.fill = TRUE, highlight = c("1","2"),show="both")
 #' while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}
 TCGAVisualize_volcano <- function(x,y,
                                   filename = "volcano.pdf",
@@ -738,20 +742,30 @@ TCGAVisualize_volcano <- function(x,y,
     # get significant data
     sig <-  y < y.cut
     sig[is.na(sig)] <- FALSE
+
+    # If x.cut
+    if(length(x.cut) == 1) {
+        x.cut.min <- -x.cut
+        x.cut.max <- x.cut
+    }
+    if(length(x.cut) == 2) {
+        x.cut.min <- x.cut[1]
+        x.cut.max <- x.cut[2]
+    }
+
     # hypermethylated/up regulated samples compared to old state
-    up <- x  > x.cut
+    up <- x  > x.cut.max
     up[is.na(up)] <- FALSE
     if (any(up & sig)) threshold[up & sig] <- "2"
 
     # hypomethylated/ down regulated samples compared to old state
-    down <-  x < (-x.cut)
+    down <-  x < x.cut.min
     down[is.na(down)] <- FALSE
     if (any(down & sig)) threshold[down & sig] <- "3"
 
     if(!is.null(highlight)){
         idx <- which(names %in% highlight)
         if(length(idx) >0 ){
-            print(idx)
             threshold[which(names %in% highlight)]  <- "4"
             color <- c(color,highlight.color)
             names(color) <- as.character(1:4)
@@ -774,9 +788,9 @@ TCGAVisualize_volcano <- function(x,y,
                 environment = .e) +
         geom_point() +
         ggtitle(title) + ylab(ylab) + xlab(xlab) +
-        geom_vline(aes(xintercept = -x.cut),
-                   colour = "black",linetype = "dashed") +
-        geom_vline(aes(xintercept = x.cut),
+        geom_vline(aes(xintercept = x.cut.min),
+                   colour = "black", linetype = "dashed") +
+        geom_vline(aes(xintercept = x.cut.max),
                    colour = "black", linetype = "dashed") +
         geom_hline(aes(yintercept = -1 * log10(y.cut)),
                    colour = "black", linetype = "dashed") +