VDJ_kmers: Calculates and plots kmers distributions and frequencies.

In alexyermanos/Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Calculates and plots kmers distributions and frequencies.

Description

Calculates and plots kmers distributions and frequencies.

Usage

VDJ_kmers(
  VDJ,
  sequence.column,
  grouping.column,
  pool.per.group,
  kmer.k,
  max.kmers,
  specific.kmers,
  plot.format,
  as.proportions
)

Arguments

VDJ	VDJ dataframe output from the VDJ_GEX_matrix function.
sequence.column	Character vector. One or more sequence column names from the VDJ for kmer counting. if more than one column is provided (e.g. c("VDJ_cdr3s_aa","VJ_cdr3s_aa")) these columns will be pasted together before counting the kmers.
grouping.column	Character. Column name of a column to group kmer counting by. This could be "sample_id" to group each kmer by the sample.
pool.per.group	Boolean. If TRUE, will sum the kmer counts of each sequence per grouping factor (determined in grouping.column).
kmer.k	Integer. Length k of each kmer.
max.kmers	Integer. Maximum number of kmers to be plotted in the output barplots.
specific.kmers	Character vector. Specific kmers to be plotted in the output barplots.
plot.format	Character. The output plot format: 'barplot' for barplots of kmer frequency per group, 'pca' for group-level PCA reduction across the kmer vectors, 'density' for kmer count density plots.
as.proportions	Boolean. If TRUE, will return the kmer barplot as proportions instead of absolute counts.

Value

Returns a ggplot with the kmer analysis depedning on the plot.format parameter

Examples

try({
 VDJ_kmers(VDJ = Platypus::small_vgm[[1]],
 sequence.column = c("VDJ_cdr3s_aa"), grouping.column = "sample_id", kmer.k = 2, max.kmers = 5)
 })

alexyermanos/Platypus documentation built on Feb. 8, 2025, 1:22 p.m.