genoHeatmap_html: Graphical output of alleles division by genotypes

Description Usage Arguments Details Value

View source: R/genoHeatmap_html.R

Description

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

Usage

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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.