ssviz (version 1.6.2)

plotDistro: plotDistro

Description

Plots distribution of reads in the bam file based on length, direction (strand) or location (rname)

Usage

plotDistro(bamlist, type = "qwidth", samplenames = NULL, unique = FALSE, ncounts = NULL, norm = FALSE, yname = "Counts per million")

Arguments

bamlist

An object of type list, giving a list of bam files. If you only have 1 file, use list(bam_file)

type

An object of type character. Can be qwidth,rname or strand. In theory, any column property existing in the bam file can be used, but these 3 would be most meaningful.

samplenames

Labels for the plot.

unique

Logical value to use unique reads (TRUE) or all reads (FALSE)

ncounts

Number of total counts in the bam file, used if unique is set to FALSE.

norm

Logical value to determine if plot will be normalised.

yname

y axis label.

Examples

data(ssviz)
plotDistro(list(ctrlbam))