geneFreq: Gene frequencies

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Creates a data frame of VDJ gene counts and frequencies.

Usage

geneFreq(productive.nt, locus = "VDJ", family = FALSE)

Arguments

productive.nt	A list of one or more data frames of productive sequences generated by the LymphoSeq function productiveSeq where the parameter aggregate is set to "nucleotide".
locus	A character vector indicating which VDJ genes to include in the output. Available options include "VDJ", "DJ", "VJ", "DJ", "V", "D", or "J".
family	A Boolean value indicating whether or not family names instead of gene names are used. If TRUE, then family names are used and if FALSE, gene names are used.

Value

Returns a data frame with the sample names, VDJ gene name, count, and % frequency of the V, D, or J genes (each gene frequency should add to 100% for each sample).

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

productive.nt <- productiveSeq(file.list = file.list, aggregate = "nucleotide")

geneFreq(productive.nt, locus = "VDJ", family = FALSE)

# Create a heat map of V gene usage
vfamilies <- geneFreq(productive.nt, locus = "V", family = TRUE)

require(reshape)

vfamilies <- reshape::cast(vfamilies, familyName ~ samples, value = "frequencyGene", sum)

rownames(vfamilies) <- as.character(vfamilies$familyName)

vfamilies$familyName <- NULL

RedBlue <- grDevices::colorRampPalette(rev(RColorBrewer::brewer.pal(11, "RdBu")))(256)

require(pheatmap)

pheatmap::pheatmap(vfamilies, color = RedBlue, scale = "row")

# Create a word cloud of V gene usage
vgenes <- geneFreq(productive.nt, locus = "V", family = FALSE)

require(wordcloud)

wordcloud::wordcloud(words = vgenes[vgenes$samples == "TRB_Unsorted_83", "geneName"], 
   freq = vgenes[vgenes$samples == "TRB_Unsorted_83", "frequencyGene"], 
	  colors = RedBlue)

# Create a cumulative frequency bar plot of V gene usage
vgenes <- geneFreq(productive.nt, locus = "V", family = FALSE)

require(ggplot2)

ggplot2::ggplot(vgenes, aes(x = samples, y = frequencyGene, fill = geneName)) +
  geom_bar(stat = "identity") +
  theme_minimal() + 
  scale_y_continuous(expand = c(0, 0)) + 
  guides(fill = guide_legend(ncol = 3)) +
  labs(y = "Frequency (%)", x = "", fill = "") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.