plot_bar_positie_nagtive: plot_bar_positie_nagtive

In dengchunyu/scPagwas: A pathway-based polygenic integration method for inferring disease-associated individual cells in single cell sequencing data

plot_bar_positie_nagtive

Description

Generate barplot of identity group composition Thanks to the SCOPfunctions package https://github.com/CBMR-Single-Cell-Omics-Platform/SCOPfunctions/blob/main/R/plot.R Generate a percentage barplot that shows the composition of each identity (e.g. sample)in terms of groups (e.g. positive and negative cells for scPagwas)

Usage

plot_bar_positie_nagtive(
  seurat_obj,
  var_ident,
  var_group,
  vec_group_colors = NULL,
  f_color = grDevices::colorRampPalette(RColorBrewer::brewer.pal(n = 11, name =
    "RdYlBu")),
  do_plot = FALSE,
  title = NULL,
  p_thre = 0.05,
  fontsize_title = 24,
  fontsize_axistitle_x = 18,
  fontsize_axistitle_y = 18,
  fontsize_axistext_x = 12,
  fontsize_axistext_y = 12,
  fontsize_legendtitle = 12,
  fontsize_legendtext = 10,
  aspect.ratio = 1.2,
  output.prefix = "Test",
  output.dirs = NULL,
  width = 7,
  height = 7
)

Arguments

seurat_obj	Seurat object (Seurat ^3.0).
var_ident	the identify variable, character.
var_group	the group variable, character.
vec_group_colors	a vector of colors, named by corresponding group. Length must match number of groups. Character.
f_color	if vec_group_colors is not provided, the user may instead provide a function f_color() that takes as its only argument the number of colors to generate.
do_plot	Whether to plot, logical.
title	NULL to leave out.
p_thre	threshold for p value.
fontsize_title	NULL to leave out.
fontsize_axistitle_x	NULL to leave out.
fontsize_axistitle_y	NULL to leave out.
fontsize_axistext_x	NULL to leave out.
fontsize_axistext_y	NULL to leave out.
fontsize_legendtitle	NULL to leave out.
fontsize_legendtext	NULL to leave out.
aspect.ratio	default is 1.2.
output.prefix	prefix for output files.
output.dirs	directory for files.
width	figure width.
height	figure height.

Value

a ggplot2 object

Examples

load(system.file("extdata", "Pagwas_data.RData", package = "scPagwas"))
plot_bar_positie_nagtive(
  seurat_obj = Pagwas_data,
  var_ident = "anno",
  var_group = "positiveCells",
  vec_group_colors = c("#E8D0B3", "#7EB5A6"),
  do_plot = FALSE
)

dengchunyu/scPagwas documentation built on Nov. 29, 2024, 2:53 p.m.