9d88e0062744b8dea79861cb32836424485f2ebd chmalee Thu Mar 18 13:10:00 2021 -0700 When overwriting barChart boxplot labels with empty value because we draw custom ones later, I forgot to override the y-label value for new vertical boxplots, refs #27149 diff --git src/hg/hgc/hgcData/barChartBoxplot.R src/hg/hgc/hgcData/barChartBoxplot.R index 870da6e..45d98ac 100644 --- src/hg/hgc/hgcData/barChartBoxplot.R +++ src/hg/hgc/hgcData/barChartBoxplot.R @@ -1,188 +1,188 @@ # Boxplot of data values by category (bar in barChart) # usage: Rscript barChartBoxplot.R itemName units colorFile dataFile outFile altName # where: # colorFile is a tab-sep file in the format: category hex-color # dataFile is a tab-sep file, with a header and row for each sample in the format: # sample category value # outFile is filename suitable for writing graphic (e.g. in PNG format) # if more than this categories, switch to a display mode that is easier to read: # - instead of plotting boxplot from left to right, plot from top to bottom # - box plot labels are horizontal # - labels and number are printed in black, not colored DENSECUTOFF <- 54 drawBoxPlot <- function(df) { # it's not easy at all in R to add optional arguments via a list object, so duplicate code if (count < DENSECUTOFF) { # old-style vertical bars with labels at a 45 degree angle. Harder to read but saves screen space yLimit <- c(-(max*.02), max+ (max*.03)) par(mar=c(marBottom,marLeft,3,1) + 0.1, mgp=c(2,1,0), font.main=1) exprPlot <- boxplot(value ~ df$category, data=df, ylab=yLabel, ylim=yLimit, main=title, col=colorsHex, border=c(darkgray), # medians medcol="black", medlwd=2, # outliers outcex=.5, outcol=darkgray, # whiskers whisklty=1, whiskcol=gray, # 'staples' staplecol=gray, staplecex=1.3, staplewex=.8, # with R versions 3.6 and later must suppress x-labels manually xlab="", # erase X axis labels (add later rotated) names=rep(c(""), count)) y1 <- par("usr")[3] size <- .8 # draw sample count twice (once in color, once in black) to make light colors readable adjust <- .4*abs(y1) text(.4, y1 + adjust, "N=", cex=size, xpd=TRUE) text(1:count, y1 + adjust, exprPlot$n, cex=size, col=colorsHex) text(1:count, y1 + adjust, exprPlot$n, cex=size, col="black") # add sample (X axis) labels at 45 degree angle rot <- 45 size <- 1 text(1:count, y1 - adjust, cex=size, labels=labels, srt=rot, xpd=TRUE, adj=c(1,.5), col="black") text(1:count, y1 - adjust, cex=size, labels=labels, srt=rot, xpd=TRUE, adj=c(1,.5), col=colorsHex) } else { # new-style vertical bars, easier to read size <- .7 longestLabelIdx = which.max(nchar(labels)) longestLabel = labels[longestLabelIdx] marLeft = nchar(longestLabel)/2.5 # 2.5 was trial and error, strwidth(longestLabel, "inches") didn't work par(mar=c(3,marLeft,2,1) + 0.1, mgp=c(2,1,0), font.main=1) yLimit <- c(-(max*.02), max+ (max*.03)) # by default, the order of horizontal barcharts is reversed compared to vertical barcharts # this is why we inverse the order with at=rev(...) and later for text() apply rev(...) on all y-coords exprPlot <- boxplot(value ~ df$category, data=df, ylim=yLimit, xlim=c(0, count), at=rev(1:nlevels(df$category)), main=title, horizontal=TRUE, space = 0.3, col=colorsHex, border=c(darkgray), # medians medcol="black", medlwd=2, # outliers outcex=.5, outcol=darkgray, # whiskers whisklty=1, whiskcol=gray, # 'staples' staplecol=gray, staplecex=1.3, staplewex=.8, # erase y ticks yaxt="n", # with R versions 3.6 and later must suppress x-labels manually - xlab="", + xlab="", ylab="" # erase X axis labels (add later rotated) names=rep(c(""), count)) y1 <- par("usr")[1] # draw numbers only black, at 90 degrees and left-adjusted rot <- 0 adjust <- .15*abs(y1) text(y1 + adjust, rev(1:count), exprPlot$n, cex=size, col="black", srt=rot, adj=0.0) # draw labels size <- .9 adjust <- .4*abs(y1) text(y1-adjust, rev(1:count), cex=size, labels=labels, srt=rot, xpd=TRUE, adj=c(1,.5), col="black") } } drawBarPlot <- function(df) { yLimit <- c(-(max*.02), max+ (max*.03)) par(mar=c(marBottom,marLeft,3,1) + 0.1, mgp=c(2.5,1,0), font.main=1) df <- df[(order(match(df$category, colorDf$category))),] exprPlot <- barplot(df$value, ylab=yLabel, ylim=yLimit, main=title, col=colorsHex, border=c(darkgray), # erase X axis labels (add later rotated) names.arg=rep(c(""), count)) limits <- par("usr") xmin <- limits[1] xmax <- limits[2] ymin <- limits[3] ymax <- limits[4] adjust <- abs(ymin) # draw box around bargraph rect(xmin, ymin + adjust, xmax, ymax, border=c(darkgray), lwd=2, xpd=TRUE) # add sample (X axis) labels at 45 degree angle rot <- 45 size <- 1 text(exprPlot, ymin - adjust, cex=size, labels=labels, srt=rot, xpd=TRUE, adj=c(1,.5), col="black") # does this have any effect? text(exprPlot, ymin - adjust, cex=size, labels=labels, srt=rot, xpd=TRUE, adj=c(1,.5), col=colorsHex) } args <- commandArgs(TRUE) locus <- args[1] units <- args[2] colorFile <- args[3] dataFile <- args[4] outFile <- args[5] name2 <- args[6] # this argument can be used by QA to check if the new fonts look very different from the old fonts # see #22838 useOldFonts <- (!is.na(args[7]) && args[7]=="1") if (!useOldFonts && require("showtext",character.only=TRUE, quietly=TRUE)) { library(showtext, quietly=TRUE) showtext_auto() showtext_opts(dpi = 72) } # read colors file colorDf = read.table(colorFile, sep="\t", header=TRUE) colorsHex <- paste("#",as.character(as.hexmode(colorDf$color)), sep="") # order categories as in colors file df <- read.table(dataFile, sep="\t", header=TRUE) df$category <- ordered(df$category, levels=colorDf$category) labels <- names(table(df$category)) count <- length(labels) # draw graph # adjust X label height based on length of labels # TODO: scale by number of categories ? if (count < DENSECUTOFF) { png(file=outFile, width=1070, height=600) } else { png(file=outFile, width=1070, height=18*count) } # res=72 is default gray <- "#A6A6A6" darkgray <- "#737373" # plot with customized margins, symbol and line styles and colors, in the style of # GTEx gene expression plots (based on GTEx Portal at the Broad) # adjust margins based on max label size marBottom <- 10; marLeft <- 4; if (max(nchar(labels)) > 30) { # change margins to appropriately fit longest label name # left * .45 + 1 accounts for final rotation and length / 3 for length to margins ratio marBottom <- max(nchar(labels))/3; marLeft <- marLeft + (marLeft * .45 + 1); } yLabel <- units max <- max(df$value) title <- locus labels = gsub("_", " ", labels) if (name2 != "n/a") title <- paste(locus, " (", name2, ")", sep="") if (length(unique(df$category)) == length(df$category)) { drawBarPlot(df) } else { drawBoxPlot(df) } graphics.off()