VDJ_rarefaction: Plots rarefaction curves for species denoted in the...

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

Plots rarefaction curves for species denoted in the feature.columns parameter across groups determined by grouping.columns

Description

Plots rarefaction curves for species denoted in the feature.columns parameter across groups determined by grouping.columns

Usage

VDJ_rarefaction(
  VDJ,
  feature.columns,
  grouping.column,
  VDJ.VJ.1chain,
  rarefaction.type,
  hill.numbers,
  number.resamples,
  sample.sizes,
  endpoint
)

Arguments

VDJ	VDJ dataframe output from the VDJ_GEX_matrix function.
feature.columns	Character vector. One or more column names from the VDJ to indicate the unique species for the rarefaction (to rarefy across). If more than one column is provided (e.g. c("VDJ_cdr3s_aa","VJ_cdr3s_aa")) these columns will be pasted together.
grouping.column	Character. Column name of a column to group the rarefaction by. This could be "sample_id" for rarefaction curves for each sample.
VDJ.VJ.1chain	Boolean defaults to TRUE. Whether to filter out aberrant cells (more than 1 VDJ or VJ chain).
rarefaction.type	Character. Options for the iNEXT rarefaction - 'sample.size','coverage.based', or 'sample.completeness'.
hill.numbers	Integer/ vector of integers. The Hill numbers to be plotted out (0 - species richness, 1 - Shannon diversity, 2 - Simpson diversity)
number.resamples	Integer. Number of bootstrap replications.
sample.sizes	Vector if integers. The sample size points at which rarefaction should be performed. Defaults to NULL
endpoint	Integer. The maximum sample size for rarefaction extrapolation. Defaults to NULL = 2 times the sample size for each sample.

Value

Returns a ggplot with the ordination analysis performer across features, groups, or both

Examples

try({
plot <- VDJ_diversity(VDJ = Platypus::small_vgm[[1]],
,feature.columns = c("VDJ_cdr3s_aa"), grouping.column = "sample_id")
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.