plot_pyprophet_protein: Read data from pyprophet and plot columns from it.

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

Read data from pyprophet and plot columns from it.

Description

More proteomics diagnostics! Now that I am looking more closely, I think this should be folded into plot_pyprophet_distribution().

Usage

plot_pyprophet_protein(
  pyprophet_data,
  column = "intensity",
  keep_real = TRUE,
  keep_decoys = FALSE,
  expt_names = NULL,
  label_chars = 10,
  protein = NULL,
  plot_title = NULL,
  scale = NULL,
  legend = NULL,
  order_by = "condition",
  show_all = TRUE,
  ...
)

Arguments

pyprophet_data	Data from extract_pyprophet_data()
column	Chosen column to plot.
keep_real	FIXME: This should be changed to something like 'data_type' here and in plot_pyprophet_distribution.
keep_decoys	Do we keep the decoys when plotting the data?
expt_names	Names for the x-axis of the plot.
label_chars	Maximum number of characters before abbreviating sample names.
protein	chosen protein(s) to plot.
plot_title	Title the plot?
scale	Put the data on a specific scale?
legend	Include the legend?
order_by	Reorder the samples by some factor, presumably condition.
show_all	Skip samples for which no observations were made.
...	Further arguments, presumably for colors or some such.

Value

Boxplot describing the desired column from the data.

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