plotTest: Plotting ribosome footprint data from mapped P-sites at the...

In jipingw/RiboDiPA: Differential pattern analysis for Ribo-seq data

Plotting ribosome footprint data from mapped P-sites at the bin level.

Description

This function visualizes the ribosome footprint in the form of mapped P-site frequency at the bin level along the total transcript. Bins that test positive for statistically significant differences are marked in black. Plotting is implmented with the ggplot2 package.

Usage

plotTest(result, genes.list = NULL, threshold = 0.05)

Arguments

result	Data object resulting from diffPatternTest or diffPatternTestExon functions or wrapper function RiboDiPA.
genes.list	genes.list is the list of genes for visualization. If genes.list is not specified, then only genes with significant differential patterns specified by q-value threshold will be plotted. If genes.list is not NULL, then threshold argument will be ignored.
threshold	The q-value threshold for genes whose footprint to be visualized. This argument is ignored if genes.list is not NULL.

Value

Bin-level tracks of genes and test results.

Examples

data(result.pst)
plotTest(result = result.pst, genes.list = NULL, threshold = 0.05)

jipingw/RiboDiPA documentation built on Dec. 10, 2024, 8:46 p.m.