plot_volcano_condition_de: Theresa's volcano plots are objectively nicer because they...

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

Theresa's volcano plots are objectively nicer because they are colored by condition.

Description

I therefore took a modified copy of her implementation and added it here.

Usage

plot_volcano_condition_de(
  input,
  table_name,
  alpha = 0.5,
  fc_col = "logFC",
  fc_name = "log2 fold change",
  line_color = "black",
  line_position = "bottom",
  logfc = 1,
  p_col = "adj.P.Val",
  p_name = "-log10 p-value",
  pval = 0.05,
  shapes_by_state = FALSE,
  color_high = "darkred",
  color_low = "darkblue",
  size = 2,
  invert = FALSE,
  label = NULL,
  label_column = "hgncsymbol",
  label_size = 6
)

Arguments

input	Table of DE values, likely from combine_de_tables().
table_name	Name the table!
alpha	Make see-through.
fc_col	Column containing the fold-change values.
fc_name	Axis label.
line_color	Color for the demarcation lines.
line_position	Put the lines above or below the dots.
logfc	Demarcation line for fold-change significance.
p_col	Column containing the significance information.
p_name	Axis label for the significance.
pval	Demarcation for (in)significance.
shapes_by_state	Change point shapes according to their states?
color_high	Color for the ups.
color_low	and the downs.
size	Point size
invert	Flip the plot?
label	Label some points?
label_column	Using this column in the data.
label_size	Use this font size for the labels on the plot.

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