barplotReadCounts: Stacked barplot of read counts

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Stacked barplot of read counts

Description

Make a stacked barplot, for instance from the output of formatReadCountsPerLane. Default graphical parameters are optimized for few categories (e.g. lanes) but many individuals.

Usage

barplotReadCounts(
  counts,
  xlab = paste0("Individuals (", ncol(counts), ")"),
  ylab = "Number of read pairs",
  main = "Read pairs per individual",
  legend.text = rownames(counts),
  col = 1:nrow(counts),
  lines.h = c(10^5, 10^6, 5 * 10^6),
  mar = c(5, 4.5, 4, 0),
  xlab.line = 3,
  font.lab = 2,
  cex.xtxt = 0.7,
  perc = FALSE,
  inset.x = -0.2
)

Arguments

counts	matrix, with categories (e.g. lanes) in rows and individuals in columns; if colnames is not NULL, they will be used as labels of the x-axis
xlab	a title for the x axis
ylab	a title for the y axis
main	an overall title for the plot
legend.text	see barplot
col	see barplot
lines.h	the y-value(s) for horizontal line(s)
mar	see par
xlab.line	see line from mtext
font.lab	see par
cex.xtxt	see cex from text
perc	if TRUE, plot data from "counts" as percentages (using prop.table), with legend on the topright outside the x-axis range, and columns (of "counts") sorted in the increasing order corresponding of the first row
inset.x	inset distance along the x axis from the margins as a fraction of the plot region

Value

invisible output of barplot

Author(s)

Timothee Flutre

Examples

## Not run: ## make fake data
(x <- matrix(data=c(10,3, 20,0, 21,17, 35,19), nrow=2, ncol=4,
             dimnames=list(c("lane1", "lane2"),
             c("ind1", "ind2", "ind3", "ind4"))))

## plot them
barplotReadCounts(counts=x)
barplotReadCounts(counts=x, perc=TRUE, ylab="Percentage of read pairs",
                  mar=c(5, 4.5, 4, 6))

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.