size.position.heatmap: Produce a heatmap of counts from the results of...

In mw55309/viRome_legacy: Analysis and visualisation of short-read sequencing data from virus-infection studies

Description

A heatmap will be drawn, the rows being read lengths, the columns being position in the genome, and the colours related to counts of read lengths mapping to those locations

Usage

size.position.heatmap(dm = NULL, minlen = 1, maxlen = 37, start = 1, end = 1e+07, scale = TRUE, col.fun = colorRampPalette(c("black", "red"), space = "rgb"), log = FALSE, mar = c(5, 4, 4, 2), main = NULL)

Arguments

dm	The output of summarise.by.length. A data.frame, the columns will be read lengths, the rows will be genome position and the values counts
minlen	The minimum length of aligned read to consider
maxlen	The maximum length of aligned read to consider
start	The minimum start position to consider
end	The maximum start position to consider
scale	Whether to scale the data for each genome position
col.fun	A function that will provide colours; could be rainbow or heat.colors etc. Defaults to colorRampPalette scaling from black to red
log	Whether to log() the data first (prior to scaling)
mar	The margins for the plot. See par. A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot.
main	A title for the plot

Value

A heatmap is drawn on the current graphical device

Author(s)

Mick Watson <[e-mail]>

Examples

 ## Not run: infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")
 ## Not run: bam <- read.bam(bamfile=infile, chr="SINV", start=1, end=11703, removeN=TRUE)
 ## Not run: bamc <- clip.bam(bam)
## Not run: dm <- summarise.by.length(bamc)
## Not run: dmp <- summarise.by.length(bamc, strand="pos")
## Not run: dmn <- summarise.by.length(bamc, strand="neg")

## Not run: size.position.heatmap(dm)
## Not run: size.position.heatmap(dm, log=TRUE, scale=FALSE)

mw55309/viRome_legacy documentation built on Dec. 21, 2021, 11:05 p.m.