genoHeatmap_html: Graphical output of alleles division by genotypes

In williamdlees/vdjbasevis: multiple visualizations for genotypes

Description

The genoHeatmap_html function generates an interactive graphical output of the alleles per gene in multiple samples.

Usage

genoHeatmap_html(
  geno_table,
  chain = c("IGH", "IGK", "IGL"),
  gene_sort = "position",
  removeIGH = TRUE,
  lk_cutoff = 1,
  mark_low_lk = TRUE,
  n_line = 4,
  line_length = 60,
  pseudo_genes = FALSE,
  ORF_genes = FALSE,
  file = file.path(normalizePath(tempdir()), "genotype_heatmap.html")
)

Arguments

geno_table	genoytpe summary table. See details.
chain	the IG chain: IGH,IGK,IGL. Default is IGH.
gene_sort	if by 'name' the genes in the output are ordered lexicographically, if by 'position' only functional genes are used and are ordered by their chromosomal location. Default is 'position'.
removeIGH	if TRUE, 'IGH'\'IGK'\'IGL' prefix is removed from gene names.
lk_cutoff	the lK cutoff value to be considerd low for texture layer. Defualt is lK<1.
mark_low_lk	if TRUE, a texture is add for low lK values. Defualt is TRUE.

Details

A data.frame created by inferGenotypeBaysian.

Value

An interactive heat-map visualization of the genotype inference for multiple samples.

williamdlees/vdjbasevis documentation built on Sept. 13, 2020, 12:17 a.m.