fcSortBarPlot_lfcShrink: The Theo Palmer Bar Plot ~for shrunken lfcs~

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

Description

Like theoBarPlot, but for shrunken LFCs.

Usage

fcSortBarPlot_lfcShrink(myResults, highlightGenes, highlightGeneName,
  fcThreshold, myTitle, myWidth, myHeight)

Arguments

myResults	Results output from DESeq (can be a data frame too I suppose, e.g. output of add_lfcShrink)
highlightGenes	column of data frame with genes you want to highlight
fcThreshold	Where do you want to draw horizontal line on plot?
myTitle	Character string representing title of plot
highlightGeneNames	Character string representing what you want highlighted genes to be called in legend
myTitle	integer representing width of plot
myTitle	integer representing height of plot

Details

Doesn't plot lfc standard error (yet).

Not only does this plot all of your differentially expressed genes as a bar plot with the Y axis representing SHRUNKEN 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.

Examples

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

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