isomiRs (version 1.0.3)

isoPlot: 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 = "condition")

Arguments

ids

object of class IsomirDataSeq

type

string (iso5, iso3, add, subs) to indicate what isomiRs to use for the plot. See details for explanation.

column

string indicating the column in colData to color samples.

Value

ggplot object showing different isomiRs changes at different positions.

Details

There are four different values for type parameter. To plot trimming at 5' or 3' end, use type="iso5" or type="iso3". In this case, it will plot 3 positions at both side of the reference position described at miRBase site. Each position refers to the number 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 number of total counts. The position at y is the number of different sequences.

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.

Examples

data(mirData)
isoPlot(mirData)