extract_coefficient_scatter: Perform a coefficient scatter plot of a...

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

Perform a coefficient scatter plot of a limma/deseq/edger/basic table.

Description

Plot the gene abundances for two coefficients in a differential expression comparison. By default, genes past 1.5 z scores from the mean are colored red/green.

Usage

extract_coefficient_scatter(
  output,
  toptable = NULL,
  type = "limma",
  x = 1,
  y = 2,
  z = 1.5,
  logfc = NULL,
  n = NULL,
  z_lines = FALSE,
  loess = FALSE,
  alpha = 0.4,
  color_low = "#DD0000",
  color_high = "#7B9F35"
)

Arguments

output	Result from the de_ family of functions, all_pairwise, or combine_de_tables().
toptable	Chosen table to query for abundances.
type	Query limma, deseq, edger, or basic outputs.
x	The x-axis column to use, either a number of name.
y	The y-axis column to use.
z	Define the range of genes to color (FIXME: extend this to p-value and fold-change).
logfc	Set a fold-change cutoff for coloring points in the scatter plot (currently not supported.)
n	Set a top-n fold-change for coloring the points in the scatter plot (this should work, actually).
z_lines	Add lines to show the z-score demarcations.
loess	Add a loess estimation (This is slow.)
alpha	How see-through to make the dots.
color_low	Color for the genes less than the mean.
color_high	Color for the genes greater than the mean.

See Also

[plot_linear_scatter()]

Examples

## Not run: 
 expt <- create_expt(metadata = "some_metadata.xlsx", gene_info = annotations)
 pairwise_output <- all_pairwise(expt)
 scatter_plot <- extract_coefficient_scatter(pairwise_output,
                                             type = "deseq", x = "uninfected", y = "infected")

## End(Not run)

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