theoBarPlot: The Theo Palmer Bar Plot

In kmuench/DESeqAid: DESeqAid: Kristin's favorite functions for her DESeq-based differential expression pipelines

Description

Not only does this plot all of your differentially expressed genes as a bar plot with the Y axis representing log2fold change, but it also orders all of the bar from positive to negative, highlights the bar corresponding to a list of interest, and draws a line at a threshold of your choosing.

Usage

theoBarPlot(myResults, highlightGenes, highlightGeneName, fcThreshold_plot,
  fcThreshold, myTitle, myWidth, myHeight)

Arguments

myResults	Results output from DESeq (not a data frame, but a DESeq object)
highlightGenes	column of data frame with genes you want to highlight
fcThreshold	Where do you want to draw horizontal line on plot? 0.58 ~= 1.5fold, 1~=2fold, 1.322~=2.5fold
myTitle	Character string representing title of plot
highlightGeneNames	Character string representing what you want highlighted genes to be called in legend

Details

NOTE: if you want to do this with SHRUNKEN LFCs, NOT THE DESEQ DEFAULT LOG2FCs, use the function theoBarPlot_lfcShrink

Examples

theoBarPlot(results_sex, amySexGenes[,1], 0.58, 0, 'Log2-Fold Change of Genes that are DE by Sex', 15, 6)

kmuench/DESeqAid documentation built on Oct. 14, 2020, 4:45 a.m.