plot_rmats: Given some psi and tpm data from rMATS, make a pretty plot!

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Given some psi and tpm data from rMATS, make a pretty plot!

Description

This should take either a dataframe or filename for the psi data from rMATS. This was mostly copy/pasted from plot_suppa().

Usage

plot_rmats(
  se = NULL,
  a5ss = NULL,
  a3ss = NULL,
  mxe = NULL,
  ri = NULL,
  sig_threshold = 0.05,
  dpsi_threshold = 0.7,
  label_type = NULL,
  alpha = 0.7
)

Arguments

se	Table of skipped exon data from rmats.
a5ss	Table of alternate 5p exons.
a3ss	Table of alternate 3p exons.
mxe	Table of alternate exons.
ri	Table of retained introns.
sig_threshold	Use this significance threshold.
dpsi_threshold	Use a delta threshold.
label_type	Choose a type of event to label.
alpha	How see-through should the points be in the plot?

Value

List containing the plot and some of the requisite data.

See Also

[plot_supps()]

Examples

 ## Not run: 
 rmats_plot <- plot_rmats(se_table, a5_table, a3_table)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.