isoPlot: Plot the amount of isomiRs in different samples

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Plot the amount of isomiRs in different samples

Description

This function plot different isomiRs proportion for each sample. It can show trimming events at both side, additions and nucleotides changes.

Usage

isoPlot(ids, type = "iso5", column = NULL, use = NULL, nts = FALSE)

Arguments

ids	Object of class IsomirDataSeq.
type	String (iso5, iso3, add, snv, all) to indicate what isomiRs to use for the plot. See details for explanation.
column	String indicating the column in colData to color samples.
use	Character vector to only use these isomiRs for the plot. The id used is the rownames that comes from using isoCounts with all the arguments on TRUE.
nts	Boolean to indicate whether plot positions of nucleotides changes when showing single nucleotides variants.

Details

There are four different values for type parameter. To plot trimming at 5' or 3' end, use type="iso5" or type="iso3". Get a summary of all using type="all". In this case, it will plot 3 positions at both side of the reference position described at miRBase site. Each position refers to the % of sequences that start/end before or after the miRBase reference. The color indicates the sample group. The size of the point is proportional to the abundance considering the total as all the sequences in the sample. The position at y is the % of different sequences considering the total as all sequences with changes for the specific isomiR showed.

Same logic applies to type="add" and type="subs". However, when type="add", the plot will refer to addition events from the 3' end of the reference position. Note that this additions don't match to the precursor sequence, they are non-template additions. In this case, only 3 positions after the 3' end will appear in the plot. When type="subs", it will appear one position for each nucleotide in the reference miRNA. Points will indicate isomiRs with nucleotide changes at the given position. When type="all" a colar coordinate map will show the abundance of each isomiR type in a single plot. Note the position is relatively to the sequence not the miRNA.

Value

ggplot2::ggplot() Object showing different isomiRs changes at different positions.

Examples

data(mirData)
isoPlot(mirData)

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.