count_plot: A function to make a plot of normalized counts

In kevincjnixon/BinfTools: Useful functions for standard analyses

A function to make a plot of normalized counts

Description

This function takes normalized counts of specific genes from a DESeq2 counts object, scales them, and creates a plot with pairwise t-tests by condition

Usage

count_plot(
  counts,
  scaling = "zscore",
  genes,
  condition,
  con = NULL,
  title = "expression",
  compare = NULL,
  col = "Dark2",
  method = "ind",
  pair = FALSE,
  pc = 1,
  yax = NULL,
  showStat = TRUE,
  style = "violin",
  sinaPoint = T,
  textsize = NULL,
  retStat = FALSE,
  retGP = FALSE
)

Arguments

counts	Normalized counts from a DESeq2 object - use 'counts(dds, normalized=TRUE)'
scaling	Method used to scale counts per gene across samples. 'zscore', 'log10', or 'none'. Default is 'zscore'
genes	Character vector of genes to subset from counts. Must correspond with rownames(counts).
condition	Character vector of conditions in DESeq2 object. Must be in order of columns (counts).
con	Character indicating the control condition. (To be displayed first in plot). Default NULL.
title	Character vector indicating title of plot. Defaults to "expression"
compare	List of character vectors (each of length 2) indicating pairwise comparisons. If NULL, all possible comparisons will be made. Default is NULL
col	Character indicating the RColorBrewer palette name or list of colours (hex, name, rgb()) to be used. Default is "Dark2"
method	Character indicating what to plot. One of "ind", "mean", "geoMean", or "median", or ".perMean". Defaults to "ind" for individual data points (one point per sample).
pair	Boolean indicating if t-test should be independent (FALSE; default) or paired (TRUE).
pc	Numeric indicating the pseudocount to be added when scaling="log10". Default=1.
yax	Character indicating the y-axis label. Leave NULL if going with default axis label.
showStat	Boolean indicating if statistics should be plotted.
style	Character indicating the style of plot ("violin", "box"). Defaults to "violin".
sinaPoint	Boolean indicating if sina points should be shown. Only when style="violin".
textsize	Numeric indicating text size for the plot. Leave NULL for default.
retStat	Boolean indicating if the stats should be returned
retGP	Boolean indicating if ggplots2 object should be returned for further editing. Default=FALSE

Value

Generates a violin or box plot

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