plot_vaf_by_clones: Plot VAF of variants across clones

In northNomad/tapestri.tools: A toolbox for the analysis of tapestri single cell multi-omics data

Plot VAF of variants across clones

Description

An in-house function used to identify multiplets in sequencing.

Usage

plot_vaf_by_clones(h5f, index_cells_list, index_variants, return_data = FALSE)

Arguments

h5f	h5f
index_cells_list	A named list of integers. The names are the names of the clones. The integers are the index of cells that belong to the corresponding clones.
return_data	Boolean. If TRUE, returns the tidy-data used for plotting
indx_variants	See get_variants_index

Value

A named list of ggplot objects, or the underlying tidy-data

Examples

#Compare IDH1_R132H VAF between wild type and mutant cells

## Not run: 
idh1mt <- get_cells_index(h5f, variants = c(IDH1_R132H = "chr2:209113112:C/T"), int_ngt = 1)
idh1wt <- get_cells_index(h5f, variants = c(IDH1_R132H = "chr2:209113112:C/T"), int_ngt = 0)
index_cells_list <- list(idh1wt = idh1wt, idh1mt = idh1mt)

plot_vaf_by_clones(h5f,
  index_cells_list = indx_ls,
  index_variants = get_variants_index(h5f, c(IDH1_R132H = "chr2:209113112:C/T"))
  )

## End(Not run)

northNomad/tapestri.tools documentation built on May 31, 2024, 4:44 p.m.