CodonHeatmap-methods: description of function heatmap

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

CodonHeatmap 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
rowGroup	a list of annotaon table columns (default = 'tRF.type.s.')
norm.type	any of 'all reads' 'all tRNA reads' or 'Unnormalized'
codon	which codon 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. 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.