Read count histogram

Plots a histogram of the marker-specific mean of log2-transformed read counts. Bounds for the definition of positive and negative controls can be highlighted by vertical lines (if given).

Usage

plotCountHist(raw, binwidth = 0.1, tZero, tPoor, tWell, title)

Arguments

raw

Raw read count matrix (rows = genes, cols = samples).

binwidth

Optional. The width of the bins as a numeric value. Default is 0.1.

tZero

Optional. Lower bound for negative controls.

tPoor

Optional. Upper bound for negative controls.

tWell

Optional. Lower bound for positive controls.

title

Plot title

xlim.max

Upper limit of the x-axis

ylim.max

Upper limit of the y-axis

Value

ggplot2 object of the read count histogram

Examples

counts <- matrix(rnbinom(1000, mu=3, size=0.01), nrow=50)
plotCountHist(counts)