plot_pyprophet_xy: Invoked plot_pyprophet_counts() twice, once for the x-axis,...

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

Invoked plot_pyprophet_counts() twice, once for the x-axis, and once for the y.

Description

Then plot the result, hopefully adding some new insights into the state of the post-pyprophet results. By default, this puts the number of identifications (number of rows) on the x-axis for each sample, and the sum of intensities on the y. Currently missing is the ability to change this from sum to mean/median/etc. That should trivially be possible via the addition of arguments for the various functions of interest.

Usage

plot_pyprophet_xy(
  pyprophet_data,
  keep_real = TRUE,
  size = 6,
  label_size = 4,
  keep_decoys = TRUE,
  expt_names = NULL,
  label_chars = 10,
  x_type = "count",
  y_type = "intensity",
  plot_title = NULL,
  scale = NULL,
  ...
)

Arguments

pyprophet_data	List of pyprophet matrices by sample.
keep_real	Use the real identifications (as opposed to the decoys)?
size	Size of the glyphs used in the plot.
label_size	Set the label sizes.
keep_decoys	Use the decoy identifications (vs. the real)?
expt_names	Manually change the labels to some other column than sample.
label_chars	Maximum number of characters in the label before shortening.
x_type	Column in the data to put on the x-axis.
y_type	Column in the data to put on the y-axis.
plot_title	Plot title.
scale	Put the data onto the log scale?
...	Extra arguments passed along.

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