plot_ma_condition_de: Create a MA plot with colors from the original expressionset.

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

Create a MA plot with colors from the original expressionset.

Description

The logic for this is directly from its volcano plot sister, but I think that function is more complete.

Usage

plot_ma_condition_de(
  input,
  table_name,
  expr_col = "logCPM",
  fc_col = "logFC",
  p_col = "qvalue",
  color_high = "red",
  color_low = "blue",
  pval = 0.05,
  alpha = 0.4,
  logfc = 1,
  label_numbers = TRUE,
  size = 2,
  shapes = TRUE,
  invert = FALSE,
  label = 10,
  label_column = "hgncsymbol",
  ...
)

Arguments

input	Result from all_pairwise() and friends.
table_name	Name the table!
expr_col	Column name from the input containing expression data.
fc_col	Ibid but the fold change column.
p_col	Ibid but the p-value.
color_high	Color for the values above the identity line.
color_low	and the low side.
pval	Significance cutoff.
alpha	Degree of see-through-ness.
logfc	Fold-change cutoff.
label_numbers	Add a legend containing counts by significance.
size	Relative size of the dots.
shapes	Use fun shapes for categories?
invert	Invert the plot?
label	Add labels for this number of genes.
label_column	Use this column for the labels.
...	Arbitrary passthrough.

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