tRF.typeHeatmap-methods: description of function heatmap

Description Arguments

Description

tRF.typeHeatmap specific for tRNAMINT data. These heatmaps should be run on size ordered objects in order to visualize the read counts of the different tRNA fragments starting from the 5' over the center to the 3' and full length fragments.

Arguments

x

the tRNAMINT object

colGroup

what do you want to have coloured at the top

norm.type

any of 'all reads' 'all tRNA reads' or 'Unnormalized'

tRF.type

which tRF.type to focus on (a column in the annotation table)

fname

the output filename

main

the title string for the heatmap default="Heatmap"

fun

collapse the data before plotting; e.g.

z.score

z.score the data after the summary (default = F)

brks

how many shades of heatmap colors ( default 10 ) function(x) { collaps(x,what='row',group='frag.type.and.length', fun = function(x) { sum( x, na.rm=TRUE) } ) }


stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.