R/plotting.R
In raerose01/deconstructSigs: Identifies Signatures Present in a Tumor Sample
Defines functions
makePie
plotTumor
plotSignatures
formatContexts
Documented in
formatContexts
makePie
plotSignatures
plotTumor
#' Formats the data for use in plotSignatures()
#'
#' Makes the contexts useable in plotSignatures()
#'
#' @keywords internal
#' @param contexts One of the entries in the output list from whichSignatures()
#' @return Returns a data frame with sample.id, full_context, fraction, and
#' mutation as column names
#' @export
formatContexts = function(contexts){
for_plotting = reshape2::melt(contexts)
colnames(for_plotting)[1] = "sample.id"
colnames(for_plotting)[2] = "full_context"
colnames(for_plotting)[3] = "fraction"
for_plotting$mutation = substr(for_plotting$full_context, 3,5)
for_plotting$full_context = as.factor(for_plotting$full_context)
for_plotting$full_context = factor(for_plotting$full_context, levels = for_plotting$full_context, ordered=T)
return(for_plotting)
}
#' Plots the result from whichSignatures()
#'
#' Uses the output from whichSignatures() and creates a plot of the given tumor
#' mutational spectrum and the calculated one
#'
#' @param sigs.output The list output from whichSignatures()
#' @param sig.type Are SBS or DBS signatures of interest?
#' @param sub A character vector that specifies cancer subtype for plot title,
#' if wanted
#' @return Plots the trinucleotide frequency for the given tumor on the top
#' panel, the calculated one on the middle panel, and the difference between
#' the two on the bottom panel.
#' @export
#' @examples
#' plotSignatures(example.output, sub = "example", sig.type = 'SBS')
plotSignatures = function(sigs.output, sig.type = 'SBS', sub = ""){
op <- graphics::par()
tumor <- sigs.output[["tumor"]]
product <- sigs.output[["product"]]
diff <- sigs.output[["diff"]]
weights <- sigs.output[["weights"]]
y_limit <- 1.2 * max(tumor, product)
tumor_plotting <- formatContexts(tumor)
product_plotting <- formatContexts(product)
error_summed <- round(sqrt(sum(diff*diff)), digits = 3)
diff_plotting <- formatContexts(diff)
name <- unique(tumor_plotting$sample.id)
subtype <- sub
tmp <- which(weights != 0)
c <- paste(colnames(weights)[tmp[1]], " : ", round(weights[tmp[1]], 3), sep = "")
if(length(tmp)>1){
for(i in tmp[2:length(tmp)]){
c <- paste(c, " & ", colnames(weights)[i], " : ", round(weights[i], 3), sep = "")
}
}
if(subtype == ''){
top.title <- name
}
if(subtype != ''){
top.title <- paste(name, " -- ", subtype, sep = "")
}
if(sig.type == 'SBS'){
graphics::par(mfrow = c(3,1), xpd = FALSE, mar=c(5, 4, 4, 2), oma=c(0,0,0,4))
grDevices::palette(c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"))
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = factor(tumor_plotting$mutation), ylim = c(0, y_limit), border = NA, space = 0.3, main = top.title, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = factor(product_plotting$mutation), ylim = c(0, y_limit), border = NA, space = 0.3, main = c, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(-y_limit, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = -y_limit, to = y_limit, by = 0.02), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = factor(diff_plotting$mutation), ylim = c(-y_limit, y_limit), border = 'black', space = 0.3, main = paste("error = ", error_summed, sep = ""), ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::par(fig=c(0,1,0,1), oma = c(1, 1, 1, 1), mar = c(0, 0, 0, 0), new = TRUE)
graphics::plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
graphics::legend('right', legend = unique(tumor_plotting$mutation), col = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"), bty = 'n', ncol = 1, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
}
if(sig.type == 'DBS'){
graphics::par(mfrow = c(3,1), xpd = FALSE, mar=c(5, 4, 4, 2), oma=c(0,0,0,4))
grDevices::palette(c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a'))
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = factor(substr(tumor_plotting$full_context,1,2)), ylim = c(0, y_limit), border = NA, space = 0.3, main = top.title, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = factor(substr(product_plotting$full_context,1,2)), ylim = c(0, y_limit), border = NA, space = 0.3, main = c, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(-y_limit, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = -y_limit, to = y_limit, by = 0.02), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = factor(substr(diff_plotting$full_context,1,2)), ylim = c(-y_limit, y_limit), border = 'black', space = 0.3, main = paste("error = ", error_summed, sep = ""), ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::par(fig=c(0,1,0,1), oma = c(1, 1, 1, 1), mar = c(0, 0, 0, 0), new = TRUE)
graphics::plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
graphics::legend('right', legend = unique(substr(tumor_plotting$full_context,1,2)), bty = 'n', col = c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a'), ncol = 1, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
}
on.exit(suppressWarnings(graphics::par(op)))
}
#' Plots a tumor profile
#'
#' Uses the output from whichSignatures() and creates a plot of the given tumor
#' mutational spectrum and the calculated one
#'
#' @param tumor A tumor matrix
#' @param sub A character vector that specifies cancer subtype for plot title,
#' if wanted
#' @return Plots the trinucleotide frequency for the given tumor
#' @export
#' @examples
#' plotTumor(example.output[['tumor']], sub = "example")
plotTumor = function(tumor, sub = ""){
op <- graphics::par()
tumor <- as.matrix(tumor)
y_limit <- 1.2 * max(tumor)
tumor_plotting <- formatContexts(tumor)
name <- as.character(unique(tumor_plotting$sample.id))
subtype <- sub
if(subtype == ''){
top.title <- name
}
if(subtype != ''){
top.title <- paste(name, " -- ", subtype, sep = "")
}
grDevices::palette(c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"))
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = factor(tumor_plotting$mutation), ylim = c(0, y_limit), border = NA, space = 0.3, main = top.title, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::legend('topright', legend = unique(tumor_plotting$mutation), col = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"), bty = 'n', ncol = 6, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
#graphics::par(fig=c(0,1,0,1), oma = c(1, 1, 1, 1), mar = c(0, 0, 0, 0), new = TRUE)
#graphics::plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
#graphics::legend('topright', legend = unique(tumor_plotting$mutation), col = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"), bty = 'n', ncol = 1, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
on.exit(suppressWarnings(graphics::par(op)))
}
#' Plots the weights from whichSignatures()
#'
#' Uses the output from whichSignatures() and creates a pie chart of the weights
#' outputted
#'
#' @param sigs.output The list output from whichSignatures()
#' @param sub A character vector that specifies cancer subtype for plot title,
#' if wanted
#' @param add.color Optional character vector to assign additional colors for
#' novel signatures
#' @return Plots a pie chart of the weights calculated in the given tumor sample
#' @export
#' @examples
#' makePie(example.output)
makePie <- function(sigs.output, sub = "", v3 = FALSE, add.color = NULL){
weights <- data.frame(sigs.output[["weights"]])
unknown <- sigs.output[["unknown"]]
weights$unknown <- unknown
# Set up all the colors possible
all.sigs <- c("Signature.1", "Signature.1A", "Signature.1B", "Signature.2", "Signature.3", "Signature.4",
"Signature.5", "Signature.6", "Signature.7", "Signature.8", "Signature.9",
"Signature.10", "Signature.11", "Signature.12", "Signature.13", "Signature.14",
"Signature.15", "Signature.16", "Signature.17", "Signature.18", "Signature.19",
"Signature.20", "Signature.21", "Signature.R1", "Signature.R2", "Signature.R3",
"Signature.U1", "Signature.U2","Signature.22", "Signature.23", "Signature.24",
"Signature.25", "Signature.26", "Signature.27", "Signature.28", "Signature.29", "Signature.30",
"unknown")
all.colors <- c("#023FA5", "#023FA5","#7D87B9","#BEC1D4","#D6BCC0","#BB7784",
"gold","#4A6FE3","#8595E1","#B5BBE3","#E6AFB9",
"#E07B91","#D33F6A","#11C638","#8DD593","#C6DEC7",
"#EAD3C6","#F0B98D","#EF9708","#0FCFC0","#9CDED6",
"#D5EAE7","#F3E1EB","#F6C4E1","#F79CD4","#866097",
"#008941","#A30059","#F6C4E1","#F79CD4","#866097",
"#008941","#A30059","#008080","#8B0000","#F4A460","#663399",
"#706563")
# giving up on color consistency
if(v3 == TRUE){
all.sigs <- c(rownames(signatures.exome.cosmic.v3.may2019), rownames(signatures.dbs.cosmic.v3.may2019), 'unknown')
tmp_color <- grep('gr(a|e)y', grDevices::colors(), invert = TRUE, value = TRUE)
all.colors <- c(tmp_color[c(405, 420, 358, 143, 427, 379, 355, 144, 123, 220,
37, 281, 211, 145, 66, 298, 41, 130, 400, 254, 242,
313, 88, 90, 81, 6, 190, 396, 181, 239, 47, 261, 346, 112,
89, 155, 158, 92, 280, 272, 98, 398, 25, 369, 131, 426, 198,
71, 334, 292, 86, 413, 46, 364, 424, 297, 73, 432, 233, 119,
174, 306, 285, 134, 430, 393, 411, 403, 165, 117, 132, 159,
397, 30, 252, 212)], '#706563')
}
all.colors <- cbind(as.data.frame(all.sigs), as.data.frame(all.colors))
colnames(all.colors) <- c("signature", "color")
# Only include weights that are not 0
ind <- which(weights > 0)
weights <- weights[,ind,drop=FALSE]
missing.colors <- colnames(weights)[!colnames(weights) %in% all.colors$signature]
if(!is.null(add.color)){
tmp <- data.frame(missing.colors, add.color)
colnames(tmp) = c('signature', 'color')
all.colors <- rbind(all.colors, tmp)
}
# Set up color palette
sigs.present <- colnames(weights)
missing.colors <- sigs.present[!sigs.present %in% all.colors$signature]
if(length(missing.colors) > 0) {
warning(paste('No color assigned for: \n', paste(missing.colors, collapse = ',\ '), '.\nTo assign one, use add.color parameter.', sep = ''))
}
colors.sigs.present = all.colors$color[match(sigs.present, all.colors$signature)]
if(sub == ''){
top.title <- rownames(weights)
}
if(sub != ''){
top.title <- paste(rownames(weights), " -- ", sub, sep = "")
}
if(length(colors.sigs.present) > 1){
grDevices::palette(as.character(colors.sigs.present))
graphics::pie(t(weights), col = factor(colnames(weights), levels = unique(colnames(weights))), labels = colnames(weights), main = top.title)
}
if(length(colors.sigs.present) == 1){
graphics::pie(t(weights), col = colors.sigs.present, labels = colnames(weights), main = top.title)
}
}
################################################
raerose01/deconstructSigs documentation built on Aug. 20, 2020, 11:44 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions makePie plotTumor plotSignatures formatContexts
Documented in formatContexts makePie plotSignatures plotTumor
#' Formats the data for use in plotSignatures()
#'
#' Makes the contexts useable in plotSignatures()
#'
#' @keywords internal
#' @param contexts One of the entries in the output list from whichSignatures()
#' @return Returns a data frame with sample.id, full_context, fraction, and
#' mutation as column names
#' @export
formatContexts = function(contexts){
for_plotting = reshape2::melt(contexts)
colnames(for_plotting)[1] = "sample.id"
colnames(for_plotting)[2] = "full_context"
colnames(for_plotting)[3] = "fraction"
for_plotting$mutation = substr(for_plotting$full_context, 3,5)
for_plotting$full_context = as.factor(for_plotting$full_context)
for_plotting$full_context = factor(for_plotting$full_context, levels = for_plotting$full_context, ordered=T)
return(for_plotting)
}
#' Plots the result from whichSignatures()
#'
#' Uses the output from whichSignatures() and creates a plot of the given tumor
#' mutational spectrum and the calculated one
#'
#' @param sigs.output The list output from whichSignatures()
#' @param sig.type Are SBS or DBS signatures of interest?
#' @param sub A character vector that specifies cancer subtype for plot title,
#' if wanted
#' @return Plots the trinucleotide frequency for the given tumor on the top
#' panel, the calculated one on the middle panel, and the difference between
#' the two on the bottom panel.
#' @export
#' @examples
#' plotSignatures(example.output, sub = "example", sig.type = 'SBS')
plotSignatures = function(sigs.output, sig.type = 'SBS', sub = ""){
op <- graphics::par()
tumor <- sigs.output[["tumor"]]
product <- sigs.output[["product"]]
diff <- sigs.output[["diff"]]
weights <- sigs.output[["weights"]]
y_limit <- 1.2 * max(tumor, product)
tumor_plotting <- formatContexts(tumor)
product_plotting <- formatContexts(product)
error_summed <- round(sqrt(sum(diff*diff)), digits = 3)
diff_plotting <- formatContexts(diff)
name <- unique(tumor_plotting$sample.id)
subtype <- sub
tmp <- which(weights != 0)
c <- paste(colnames(weights)[tmp[1]], " : ", round(weights[tmp[1]], 3), sep = "")
if(length(tmp)>1){
for(i in tmp[2:length(tmp)]){
c <- paste(c, " & ", colnames(weights)[i], " : ", round(weights[i], 3), sep = "")
}
}
if(subtype == ''){
top.title <- name
}
if(subtype != ''){
top.title <- paste(name, " -- ", subtype, sep = "")
}
if(sig.type == 'SBS'){
graphics::par(mfrow = c(3,1), xpd = FALSE, mar=c(5, 4, 4, 2), oma=c(0,0,0,4))
grDevices::palette(c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"))
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = factor(tumor_plotting$mutation), ylim = c(0, y_limit), border = NA, space = 0.3, main = top.title, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = factor(product_plotting$mutation), ylim = c(0, y_limit), border = NA, space = 0.3, main = c, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(-y_limit, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = -y_limit, to = y_limit, by = 0.02), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = factor(diff_plotting$mutation), ylim = c(-y_limit, y_limit), border = 'black', space = 0.3, main = paste("error = ", error_summed, sep = ""), ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::par(fig=c(0,1,0,1), oma = c(1, 1, 1, 1), mar = c(0, 0, 0, 0), new = TRUE)
graphics::plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
graphics::legend('right', legend = unique(tumor_plotting$mutation), col = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"), bty = 'n', ncol = 1, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
}
if(sig.type == 'DBS'){
graphics::par(mfrow = c(3,1), xpd = FALSE, mar=c(5, 4, 4, 2), oma=c(0,0,0,4))
grDevices::palette(c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a'))
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = factor(substr(tumor_plotting$full_context,1,2)), ylim = c(0, y_limit), border = NA, space = 0.3, main = top.title, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(product_plotting$fraction, names.arg = product_plotting$full_context, cex.names = 0.7, las = 2, col = factor(substr(product_plotting$full_context,1,2)), ylim = c(0, y_limit), border = NA, space = 0.3, main = c, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(-y_limit, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = -y_limit, to = y_limit, by = 0.02), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(diff_plotting$fraction, names.arg = diff_plotting$full_context, cex.names = 0.7, las = 2, col = factor(substr(diff_plotting$full_context,1,2)), ylim = c(-y_limit, y_limit), border = 'black', space = 0.3, main = paste("error = ", error_summed, sep = ""), ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::par(fig=c(0,1,0,1), oma = c(1, 1, 1, 1), mar = c(0, 0, 0, 0), new = TRUE)
graphics::plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
graphics::legend('right', legend = unique(substr(tumor_plotting$full_context,1,2)), bty = 'n', col = c('#a6cee3','#1f78b4','#b2df8a','#33a02c','#fb9a99','#e31a1c','#fdbf6f','#ff7f00','#cab2d6','#6a3d9a'), ncol = 1, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
}
on.exit(suppressWarnings(graphics::par(op)))
}
#' Plots a tumor profile
#'
#' Uses the output from whichSignatures() and creates a plot of the given tumor
#' mutational spectrum and the calculated one
#'
#' @param tumor A tumor matrix
#' @param sub A character vector that specifies cancer subtype for plot title,
#' if wanted
#' @return Plots the trinucleotide frequency for the given tumor
#' @export
#' @examples
#' plotTumor(example.output[['tumor']], sub = "example")
plotTumor = function(tumor, sub = ""){
op <- graphics::par()
tumor <- as.matrix(tumor)
y_limit <- 1.2 * max(tumor)
tumor_plotting <- formatContexts(tumor)
name <- as.character(unique(tumor_plotting$sample.id))
subtype <- sub
if(subtype == ''){
top.title <- name
}
if(subtype != ''){
top.title <- paste(name, " -- ", subtype, sep = "")
}
grDevices::palette(c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"))
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = NA, ylim = c(0, y_limit), border = NA, xaxt='n', ann=FALSE, yaxt = 'n', space = 0.3)
graphics::box()
x = graphics::par('usr')
graphics::abline(h = seq(from = 0, to = y_limit, by = 0.01), col = '#d3d3d350', lty = 1)
graphics::abline(v = seq(from = x[1], to = x[2], by = 1), col = '#d3d3d350', lty = 1)
graphics::barplot(tumor_plotting$fraction, names.arg = tumor_plotting$full_context, cex.names = 0.7, las = 2, col = factor(tumor_plotting$mutation), ylim = c(0, y_limit), border = NA, space = 0.3, main = top.title, ylab = 'fraction', add = TRUE, ann = TRUE)
graphics::legend('topright', legend = unique(tumor_plotting$mutation), col = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"), bty = 'n', ncol = 6, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
#graphics::par(fig=c(0,1,0,1), oma = c(1, 1, 1, 1), mar = c(0, 0, 0, 0), new = TRUE)
#graphics::plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
#graphics::legend('topright', legend = unique(tumor_plotting$mutation), col = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2"), bty = 'n', ncol = 1, inset=c(-0,0), pch = 15, xpd = TRUE, pt.cex = 2.5)
on.exit(suppressWarnings(graphics::par(op)))
}
#' Plots the weights from whichSignatures()
#'
#' Uses the output from whichSignatures() and creates a pie chart of the weights
#' outputted
#'
#' @param sigs.output The list output from whichSignatures()
#' @param sub A character vector that specifies cancer subtype for plot title,
#' if wanted
#' @param add.color Optional character vector to assign additional colors for
#' novel signatures
#' @return Plots a pie chart of the weights calculated in the given tumor sample
#' @export
#' @examples
#' makePie(example.output)
makePie <- function(sigs.output, sub = "", v3 = FALSE, add.color = NULL){
weights <- data.frame(sigs.output[["weights"]])
unknown <- sigs.output[["unknown"]]
weights$unknown <- unknown
# Set up all the colors possible
all.sigs <- c("Signature.1", "Signature.1A", "Signature.1B", "Signature.2", "Signature.3", "Signature.4",
"Signature.5", "Signature.6", "Signature.7", "Signature.8", "Signature.9",
"Signature.10", "Signature.11", "Signature.12", "Signature.13", "Signature.14",
"Signature.15", "Signature.16", "Signature.17", "Signature.18", "Signature.19",
"Signature.20", "Signature.21", "Signature.R1", "Signature.R2", "Signature.R3",
"Signature.U1", "Signature.U2","Signature.22", "Signature.23", "Signature.24",
"Signature.25", "Signature.26", "Signature.27", "Signature.28", "Signature.29", "Signature.30",
"unknown")
all.colors <- c("#023FA5", "#023FA5","#7D87B9","#BEC1D4","#D6BCC0","#BB7784",
"gold","#4A6FE3","#8595E1","#B5BBE3","#E6AFB9",
"#E07B91","#D33F6A","#11C638","#8DD593","#C6DEC7",
"#EAD3C6","#F0B98D","#EF9708","#0FCFC0","#9CDED6",
"#D5EAE7","#F3E1EB","#F6C4E1","#F79CD4","#866097",
"#008941","#A30059","#F6C4E1","#F79CD4","#866097",
"#008941","#A30059","#008080","#8B0000","#F4A460","#663399",
"#706563")
# giving up on color consistency
if(v3 == TRUE){
all.sigs <- c(rownames(signatures.exome.cosmic.v3.may2019), rownames(signatures.dbs.cosmic.v3.may2019), 'unknown')
tmp_color <- grep('gr(a|e)y', grDevices::colors(), invert = TRUE, value = TRUE)
all.colors <- c(tmp_color[c(405, 420, 358, 143, 427, 379, 355, 144, 123, 220,
37, 281, 211, 145, 66, 298, 41, 130, 400, 254, 242,
313, 88, 90, 81, 6, 190, 396, 181, 239, 47, 261, 346, 112,
89, 155, 158, 92, 280, 272, 98, 398, 25, 369, 131, 426, 198,
71, 334, 292, 86, 413, 46, 364, 424, 297, 73, 432, 233, 119,
174, 306, 285, 134, 430, 393, 411, 403, 165, 117, 132, 159,
397, 30, 252, 212)], '#706563')
}
all.colors <- cbind(as.data.frame(all.sigs), as.data.frame(all.colors))
colnames(all.colors) <- c("signature", "color")
# Only include weights that are not 0
ind <- which(weights > 0)
weights <- weights[,ind,drop=FALSE]
missing.colors <- colnames(weights)[!colnames(weights) %in% all.colors$signature]
if(!is.null(add.color)){
tmp <- data.frame(missing.colors, add.color)
colnames(tmp) = c('signature', 'color')
all.colors <- rbind(all.colors, tmp)
}
# Set up color palette
sigs.present <- colnames(weights)
missing.colors <- sigs.present[!sigs.present %in% all.colors$signature]
if(length(missing.colors) > 0) {
warning(paste('No color assigned for: \n', paste(missing.colors, collapse = ',\ '), '.\nTo assign one, use add.color parameter.', sep = ''))
}
colors.sigs.present = all.colors$color[match(sigs.present, all.colors$signature)]
if(sub == ''){
top.title <- rownames(weights)
}
if(sub != ''){
top.title <- paste(rownames(weights), " -- ", sub, sep = "")
}
if(length(colors.sigs.present) > 1){
grDevices::palette(as.character(colors.sigs.present))
graphics::pie(t(weights), col = factor(colnames(weights), levels = unique(colnames(weights))), labels = colnames(weights), main = top.title)
}
if(length(colors.sigs.present) == 1){
graphics::pie(t(weights), col = colors.sigs.present, labels = colnames(weights), main = top.title)
}
}
################################################
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.