plotSamplesByName: Plots expression distributions of genes selected by name

In jsieker/DipEx: Analysis of RNAseq data distributions through visualization and Hartigan's Dip test

Description

Allows the user to plot the expression distributions of up to 8 genes of their choice.

Usage

plotSamplesByName(nameList, RNAdata)

Arguments

nameList	The names of the desired genes should be concatenated into this variable. If more than eight gene names are specified, function will typically fail. (ex. li <- c("Ascl3", "Bambi", "Pols2")) ). Pay very close attention to proper capitalization in specifying gene names. Any error in capitalization or erroneously-placed spaces will cause the function to fail.
RNAdata	This argument specifies the RNAseq dataset from which the specified genes' expressional data will be taken. It may take the form of raw or normalized data. Columns with non-numerical data (or containing data not relating to a sample) should be specifically exempted before any analysis is attempted.

Value

A single plot is the output of this function.

Author(s)

Software authors: Jeremy Sieker, Sohyon Lee, Kristin Baldwin

References

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2009.

Examples

x <- paste("https://www.ebi.ac.uk/gxa/experiments-content",
  "/E-GEOD-70484/resources/BaselineProfilesWriterService.RnaSeq/tsv", sep = "")
ss <- read.table(url(x),sep = '\t', header = TRUE)
ss <- ss[(as.numeric(row.names(ss)) %% 2 == 1),]
#if the previous line fails, remove the slashes from the modulo division and try again
row.names(ss) <- ss$Gene.ID #cutting it in half to speed up the examples
ss <- ss[,-c(1:2)] #removing everything that is not expression data

geneList <- row.names(ss[sample(nrow(ss), 4), ]) #get some random gene names
mod4 <- plotSamplesByName(nameList = geneList, RNAdata = ss)

jsieker/DipEx documentation built on May 17, 2019, 2:10 p.m.