Merge pull request #157 from uclahs-cds/hwinata-clone-genome-snv-count

Clone genome snv count
uclahs-cds · Nov 13, 2024 · 030bb7c · 030bb7c
2 parents 97210b4 + 7a9cfa0
commit 030bb7c
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Showing 10 changed files with 49 additions and 26 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -11,6 +11,7 @@
 * Add parameters to specify polygon shape and width.
 * Add option to use scale bars instead of y-axes.
 * Wrapper function for `SRCgrob` to automatically save plots to file
+* * Add option to annotate the CCF summary heatmap with the cell values.
 
 ## Update
 * Fixed angle calculation bug where child angles do not follow
@@ -23,6 +24,7 @@
 * Set default parameters for heatmaps, defaulting to BPG defaults unless necessary
 * Improved default node style
 * Define color scheme with a single value, automatically generating other shades.
+* Report the number of SNVs per clone in the legend for the clone-genome distribution plot.
 
 ## Bug
 * Resolved issue where the spread parameter was not applied in dendrogram mode.

diff --git a/R/SRCGrob.R b/R/SRCGrob.R
@@ -45,7 +45,7 @@ SRCGrob <- function(
 
     node.col <- 'white';
     if (length(colour.scheme) == 1) {
-        colour.scheme <- BoutrosLab.plotting.general::colour.gradient(colour.scheme, nrow(tree));
+        colour.scheme <- c(NA, BoutrosLab.plotting.general::colour.gradient(colour.scheme, nrow(tree)));
         }
 
     inputs <- prep.tree(

diff --git a/R/create.ccf.heatmap.R b/R/create.ccf.heatmap.R
@@ -4,7 +4,7 @@ create.ccf.heatmap <- function(
     clustering.method = 'complete',
     distance.method = 'euclidean',
     xaxis.lab = '',
-    xlab.label = 'Mutations',
+    xlab.label = 'SNVs',
     print.colour.key = FALSE,
     colour.scheme = c('white', 'blue'),
     ...

diff --git a/R/create.ccf.summary.heatmap.R b/R/create.ccf.summary.heatmap.R
@@ -20,6 +20,7 @@ create.ccf.summary.heatmap <- function(
     legend.x = 0.9,
     legend.y = 0.8,
     plot.objects.heights = c(0.3, 1),
+    add.median.text = FALSE,
     ...
     ) {
 
@@ -91,16 +92,16 @@ create.ccf.summary.heatmap <- function(
         xat = sample.xaxis$at
         );
 
-    hm <- BoutrosLab.plotting.general::create.heatmap(
+    hm.args <- list(
         x = arr,
         cluster.dimensions = 'none',
-        xlab.label = 'Clone ID',
+        xlab.label = 'Clone',
         xlab.cex = ifelse(is.null(clone.colours), subplot.xlab.cex, 0),
         xaxis.lab = rownames(arr),
         xaxis.cex = ifelse(is.null(clone.colours), subplot.xaxis.cex, 0),
         xaxis.fontface = subplot.xaxis.fontface,
         xaxis.rot = hm.xaxis.rot,
-        ylab.label = 'Sample ID',
+        ylab.label = 'Sample',
         ylab.cex = subplot.ylab.cex,
         yaxis.lab = colnames(arr),
         yaxis.cex = subplot.yaxis.cex,
@@ -109,11 +110,21 @@ create.ccf.summary.heatmap <- function(
         colour.scheme = hm.col.scheme
         );
 
+    if (add.median.text) {
+        contrast.thres <- (diff(range(arr)) * 0.8) + min(arr);
+        hm.args$cell.text <- round(arr[arr > 0], 2);
+        hm.args$row.pos <- which(arr > 0, arr.ind = TRUE)[,2];
+        hm.args$col.pos <- which(arr > 0, arr.ind = TRUE)[,1];
+        hm.args$text.col <- ifelse(arr > contrast.thres, 'white', 'black');
+        }
+
+    hm <- do.call(BoutrosLab.plotting.general::create.heatmap, hm.args);
+
     legend.ccf <- BoutrosLab.plotting.general::legend.grob(
         list(
             legend = list(
                 title = 'CCF',
-                labels = c(min(arr), rep('', legend.size), max(arr)),
+                labels = c(signif(min(arr), 2), rep('', legend.size), signif(max(arr), 2)),
                 colours = c('white', 'blue'),
                 border = 'black',
                 continuous = TRUE,
@@ -128,7 +139,7 @@ create.ccf.summary.heatmap <- function(
     if (!is.null(clone.colours)) {
         clone.cov <- BoutrosLab.plotting.general::create.heatmap(
             x = t(clone.colours[rownames(arr)]),
-            xlab.label = 'Clone ID',
+            xlab.label = 'Clone',
             xlab.cex = subplot.xlab.cex,
             xaxis.lab = rownames(arr),
             xaxis.cex = subplot.xaxis.cex,

diff --git a/R/create.clone.genome.distribution.plot.R b/R/create.clone.genome.distribution.plot.R
@@ -25,11 +25,11 @@ create.clone.genome.distribution.plot <- function(
             stop('ID column must contain sample ID if multi.sample is TRUE');
             }
         # filename must be a directory
-        if (!dir.exists(filename)) {
+        if (!is.null(filename) && !dir.exists(filename)) {
             stop('filename must be a directory if multi.sample is TRUE');
             }
     } else {
-        if (dir.exists(filename)) {
+        if (!is.null(filename) && dir.exists(filename)) {
             stop('filename must be a path (not a directory) if multi.sample is FALSE');
             }
         snv.df$ID <- 'all';
@@ -46,29 +46,31 @@ create.clone.genome.distribution.plot <- function(
     chr.info <- genome.pos.df$chr.info;
     chr.info$xat <- (chr.info$length / 2) + chr.info$start;
 
+    plt.list <- list();
     for (s in unique(snv.df$ID)) {
         # Iterate through each sample -------------------------------------------------------------
         print(paste('Plotting clone distribution across the genome for sample:', s));
 
         sample.df <- droplevels(snv.df[snv.df$ID == s, ]);
         sample.df <- unique(sample.df[, c('clone.id', 'genome.pos', 'SNV.id', 'ID')]);
-        if (multi.sample & !is.null(filename)) {
+        if (!is.null(filename) && multi.sample) {
             save.plt <- file.path(filename, paste0(s, '.png'));
         } else {
             save.plt <- filename;
             }
 
-        plt <- create.clone.genome.distribution.plot.per.sample(
+        plt.list[[s]] <- create.clone.genome.distribution.plot.per.sample(
             sample.df,
             clone.colours[levels(sample.df$clone.id)],
             chr.info,
-            save.plt = ifelse(is.null(filename), NULL, save.plt),
+            save.plt = save.plt,
             alpha = alpha,
             legend.x = legend.x,
             legend.y = legend.y,
             ...
             );
         }
+    return(plt.list);
     }
 
 create.clone.genome.distribution.plot.per.sample <- function(
@@ -98,7 +100,7 @@ create.clone.genome.distribution.plot.per.sample <- function(
     # calculate densities for each cluster --------------------------------------------------------
     density.list <- list();
     for (k in unique(sample.df$clone.id)) {
-        if (sum(sample.df$clone.id == k) <= 1) {
+        if (sum(sample.df$clone.id == k, na.rm = TRUE) <= 1) {
             warning(paste('Skipping clone', k, 'in sample', unique(sample.df$ID), 'since there is only one SNV'));
             next;
         }
@@ -109,17 +111,22 @@ create.clone.genome.distribution.plot.per.sample <- function(
     density.df <- do.call(rbind, density.list);
 
     # get plot legend -----------------------------------------------------------------------------
+    legend.label <- sapply(names(clone.colours), function(k) {
+        nsnv <- length(unique(sample.df[sample.df$clone.id == k, ]$SNV.id));
+        return(paste0(k, ' (', nsnv, ')'));
+        });
     clone.colours <- clone.colours[levels(sample.df$clone.id)];
     cluster.legend <- BoutrosLab.plotting.general::legend.grob(
         list(
             legend = list(
-                title = 'Clone ID',
-                labels = names(clone.colours),
+                title = 'Clone (SNVs)',
+                labels = legend.label[names(clone.colours)],
                 colours = c(clone.colours),
                 border = 'black'
                 )
             ),
         size = legend.size,
+        title.just = 'left',
         title.cex = legend.title.cex,
         label.cex = legend.label.cex
         );

diff --git a/R/create.clone.genome.distribution.scatterplot.R b/R/create.clone.genome.distribution.scatterplot.R
@@ -12,9 +12,7 @@ create.clone.genome.distribution.scatterplot <- function(
         filename = save.plt,
         formula = clone.id ~ genome.pos,
         data = scatter.df,
-        xlab.top.lab = paste0('Total SNVs: ', nsnv),
-        xlab.top.y = 0.5,
-        ylab.label = 'Clone ID',
+        ylab.label = 'Clone',
         xaxis.lab = chr.info$chr,
         yaxis.lab = levels(scatter.df$clone.id),
         xat = chr.info$xat,

diff --git a/R/create.cluster.heatmap.R b/R/create.cluster.heatmap.R
@@ -9,6 +9,7 @@ create.cluster.heatmap <- function(
     legend.title.cex = 1.2,
     legend.label.cex = 1,
     filename = NULL,
+    xlab.label = 'SNVs',
     xlab.cex = 1.2,
     xaxis.cex = 1,
     xaxis.fontface = 'bold',
@@ -54,7 +55,7 @@ create.cluster.heatmap <- function(
 
     cov <- BoutrosLab.plotting.general::create.heatmap(
         x = t(clone.colours[snv.order$clone.id]),
-        xlab.label = 'Mutations',
+        xlab.label = xlab.label,
         xlab.cex =  xlab.cex,
         xaxis.cex = xaxis.cex,
         xaxis.fontface = xaxis.fontface,
@@ -69,14 +70,14 @@ create.cluster.heatmap <- function(
         list(
             legend = list(
                 title = 'CCF',
-                labels = c(min(arr), rep('', legend.size), max(arr)),
+                labels = c(signif(min(arr), 2), rep('', legend.size), signif(max(arr), 2)),
                 colours = colour.scheme,
                 border = 'black',
                 continuous = TRUE,
                 cex = legend.label.cex
                 ),
             legend = list(
-                title = 'Clone ID',
+                title = 'Clone',
                 labels = names(clone.colours),
                 colours = clone.colours,
                 border = 'black',

diff --git a/man/create.ccf.heatmap.Rd b/man/create.ccf.heatmap.Rd
@@ -11,7 +11,7 @@ create.ccf.heatmap(
     clustering.method = 'complete',
     distance.method = 'euclidean',
     xaxis.lab = '',
-    xlab.label = 'Mutations',
+    xlab.label = 'SNVs',
     print.colour.key = FALSE,
     colour.scheme = c('white', 'blue'),
     ...
@@ -23,11 +23,11 @@ create.ccf.heatmap(
     \item{clustering.method}{Defaults to \dQuote{complete}.}
     \item{distance.method}{Defaults to \dQuote{euclidean}.}
     \item{xaxis.lab}{Defaults to an empty string.}
-    \item{xlab.label}{Defaults to \dQuote{Mutations}.}
+    \item{xlab.label}{Defaults to \dQuote{SNVs}.}
     \item{print.colour.key}{Defaults to \code{FALSE}.}
     \item{colour.scheme}{Defaults to \code{c('white', 'blue')}.}
     \item{...}{Pass through argument. See BoutrosLab.plotting.general::create.heatmap() for further details.}
 }
 \value{A `grob` object of the heatmap.}
 \author{Helena Winata}
-\seealso{\code{\link[BoutrosLab.plotting.general]{create.heatmap}}}
+\seealso{\code{\link[BoutrosLab.plotting.general]{create.heatmap}}}
diff --git a/man/create.ccf.summary.heatmap.Rd b/man/create.ccf.summary.heatmap.Rd
@@ -28,6 +28,7 @@ create.ccf.summary.heatmap(
     legend.x = 0.9,
     legend.y = 0.8,
     plot.objects.heights = c(0.3, 1),
+    add.median.text = FALSE,
     ...
     );
 }
@@ -53,9 +54,10 @@ create.ccf.summary.heatmap(
     \item{legend.x}{Legend parameter. Defaults to 0.9}
     \item{legend.y}{Legend parameter. Defaults to 0.8}
     \item{plot.objects.heights}{If \code{clone.colours} is specified, this must be an array of length 3. Defaults to \code{c(0.3, 1)}. See BoutrosLab.plotting.general::create.multipanelplot()}
+    \item{add.median.text}{If \code{TRUE}, median CCF values will be added to the heatmap. Defaults to \code{FALSE}}
     \item{...}{Pass through argument. See BoutrosLab.plotting.general::create.multipanelplot() for further details.}
 
 }
 \value{A `grob` object of the summary plot.}
 \author{Helena Winata}
-\seealso{\code{\link[BoutrosLab.plotting.general]{legend.grob}}, \code{\link[BoutrosLab.plotting.general]{create.multipanelplot}}, \code{\link[BoutrosLab.plotting.general]{create.heatmap}}}
+\seealso{\code{\link[BoutrosLab.plotting.general]{legend.grob}}, \code{\link[BoutrosLab.plotting.general]{create.multipanelplot}}, \code{\link[BoutrosLab.plotting.general]{create.heatmap}}}
diff --git a/man/create.cluster.heatmap.Rd b/man/create.cluster.heatmap.Rd
@@ -16,6 +16,7 @@ create.cluster.heatmap(
     legend.title.cex = 1.2,
     legend.label.cex = 1,
     filename = NULL,
+    xlab.label = 'SNVs',
     xlab.cex = 1.2,
     xaxis.cex = 1,
     xaxis.fontface = 'bold',
@@ -35,6 +36,7 @@ create.cluster.heatmap(
     \item{legend.title.cex}{Size of titles in the legends. Defaults to 1.2}
     \item{legend.label.cex}{Size of text labels in the legends. Defaults to 1}
     \item{filename}{Filename for tiff output, or if NULL returns the trellis object itself. Defaults to \code{NULL}.}
+    \item{xlab.label}{Defaults to \dQuote{SNVs}.}
     \item{xlab.cex}{Defaults to 1.2}
     \item{xaxis.cex}{Defaults to 1}
     \item{xaxis.fontface}{Defaults to \dQuote{bold}.}
@@ -44,4 +46,4 @@ create.cluster.heatmap(
 }
 \value{A `grob` object of the heatmap.}
 \author{Helena Winata}
-\seealso{\code{\link{create.ccf.heatmap}}, \code{\link[BoutrosLab.plotting.general]{create.heatmap}}}
+\seealso{\code{\link{create.ccf.heatmap}}, \code{\link[BoutrosLab.plotting.general]{create.heatmap}}}