plot_suppa: Given some psi and tpm data, make a pretty plot!

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

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

Description

This should take either a dataframe or filename for the psi data from suppa, along with the same for the average log tpm data (acquired from suppa diffSplice with –save_tpm_events)

Usage

plot_suppa(
  file_prefix,
  file_list = NULL,
  type = "type",
  annot = NULL,
  annot_column = NULL,
  sig_threshold = 0.05,
  label_type = NULL,
  alpha = 0.3,
  numerator = "infected",
  denominator = "uninfected"
)

Arguments

file_prefix	Directory containing the various requisite input files.
file_list	Vector of filenames.
type	Either transcript or 'type' referring to the type of DPSI analysis performed.
annot	Dataframe of annotations.
annot_column	Column in annot with the IDs to cross reference against.
sig_threshold	Use this significance threshold.
label_type	Choose a type of event to label.
alpha	How see-through should the points be in the plot?
numerator	Name of the desired comparison's numerator.
denominator	Name of the desired comparison's denominator.

Value

List containing the plot and some of the requisite data.

See Also

[plot_rmats()]

Examples

 ## Not run: 
 suppa_plot <- plot_suppa(dpsi_file, tmp_file)

## End(Not run)

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