barGene: Create a bar plot of gene expression

In kevincjnixon/BinfTools: Useful functions for standard analyses

Create a bar plot of gene expression

Description

This function will accept a list of genes and counts to produce a bar plot of gene expression in different conditions

Usage

barGene(
  genes,
  counts,
  conditions,
  title = "Gene expression",
  norm = NULL,
  eb = "sd",
  returnDat = FALSE,
  col = "Dark2",
  ord = NULL,
  con = NULL,
  stat.test = "t.test",
  hide.ns = TRUE,
  retGP = FALSE
)

Arguments

genes	character vector of genes to plot. Must match rownames(counts)
counts	count matrix of gene expression, where rows are genes and columns are samples
conditions	character vector of length ncol(counts) describing the condition of each sampmle in counts
title	character describing the title of the plot
norm	character describing the condition to use as a reference for relative gene expression. Each gene's expression will be set relative to this condition. Leave 'NULL' if plotting raw values.
eb	character describing the style of error bar. "sd" = standard deviation, "se" = standard error of the mean. Use '0' if no error bars to be plotted. Default is 'sd'.
returnDat	Boolean indicating if list of raw and summarized data should be returned for further analysis. Default is FALSE.
col	character indicating the RColorBrewer palette name or list of colours (hex, name, rgb()) to be used. Default is "Dark2"
ord	character indicating the order in which the samples should appear (overrides any ordering from using 'norm' argument). Default is NULL.
con	character indicating control condition if pairswise t-tests are to be performed. Leave NULL to not include stats. Set to 'show.all' to show all pairwise comparisons within each gene.
stat.test	character indicating either "t.test" or "wilcox" for stats when 'con' is defined. Default is "t.test"
hide.ns	logical value. If TRUE, hide ns symbol when displaying significance levels.
retGP	logical indicating if ggplot object should be returned. Default is FALSE.

Value

Bar plot of gene expression and list of length 2 containing 'rawData' and 'Summary' of gene expression data if 'returnDat' is TRUE.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.