plot_significant_bar: Plot significant genes by contrast with different colors for...

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

Plot significant genes by contrast with different colors for significance levels.

Description

This is my attempt to recapitulate some plots made in Laura and Najib's mbio paper. The goal of the plot is to show a few ranges of significance as differently colored and stacked bars. The colors are nice because Najib and Laura chose them.

Usage

plot_significant_bar(
  ups,
  downs,
  maximum = NULL,
  text = TRUE,
  color_list = c("lightcyan", "lightskyblue", "dodgerblue", "plum1", "orchid", "purple4"),
  color_names = c("a_up_inner", "b_up_middle", "c_up_outer", "a_down_inner",
    "b_down_middle", "c_down_outer")
)

Arguments

ups	Set of up-regulated genes.
downs	Set of down-regulated genes.
maximum	Maximum/minimum number of genes to display.
text	Add text at the ends of the bars describing the number of genes >/< 0 fc.
color_list	Set of colors to use for the bars.
color_names	Categories associated with aforementioned colors.

Value

weird significance bar plots

See Also

[ggplot2] [extract_significant_genes()]

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