extract_de_plots: Make a MA plot of some limma output with pretty colors and...

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

Make a MA plot of some limma output with pretty colors and shapes.

Description

Yay pretty colors and shapes! This function should be reworked following my rewrite of combine_de_tables(). It is certainly possible to make the logic here much simpler now.

Usage

extract_de_plots(
  pairwise,
  combined = NULL,
  type = NULL,
  invert = FALSE,
  invert_colors = c(),
  numerator = NULL,
  denominator = NULL,
  alpha = 0.4,
  z = 1.5,
  n = NULL,
  logfc = 1,
  pval = 0.05,
  adjp = TRUE,
  found_table = NULL,
  p_type = "adj",
  color_high = NULL,
  color_low = NULL,
  loess = FALSE,
  z_lines = FALSE,
  label = 10,
  label_column = "hgncsymbol"
)

Arguments

pairwise	The result from all_pairwise(), which should be changed to handle other invocations too.
combined	Result from one of the combine_de_table functions.
type	Type of table to use: deseq, edger, limma, basic.
invert	Invert the plot?
invert_colors	vector of new colors.
numerator	Use this factor as the numerator.
denominator	Use this factor as the denominator.
alpha	Use this transparency.
z	z-score cutoff for coefficient significance.
n	Choose the top/bottom-n by logFC.
logfc	What logFC to use for the MA plot horizontal lines.
pval	Cutoff to define 'significant' by p-value.
adjp	Use adjusted p-value?
found_table	Result from edger to use, left alone it chooses the first.
p_type	Adjusted or raw pvalues?
color_high	Color to use for the 'high' genes.
color_low	Color to use for the 'low' genes.
loess	Add a loess estimator to the coefficient plot?
z_lines	Add the z-score lines?
label	Label this number of top-diff genes.
label_column	Use this column for labelling genes.

Value

a plot!

See Also

[plot_ma_de()] [plot_volcano_de()]

Examples

## Not run: 
 prettyplot <- edger_ma(all_aprwise) ## [sic, I'm witty! and can speel]

## End(Not run)

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