genoHeatmap: Graphical output of alleles division by genotypes

In williamdlees/vdjbasevis: multiple visualizations for genotypes

Description

The genoHeatmap function generates a graphical output of the alleles per gene in multiple samples.

Usage

genoHeatmap(
  geno_table,
  chain = c("IGH", "IGK", "IGL"),
  gene_sort = "position",
  removeIGH = TRUE,
  lk_cutoff = 1,
  mark_low_lk = TRUE,
  html = FALSE,
  n_line = 4,
  line_length = 60,
  pseudo_genes = FALSE,
  ORF_genes = FALSE,
  file = NULL,
  color_y = NULL
)

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.
file	file path for rendering the plot to pdf. If non is supplied than the plot is retured as object. Defualt is NULL.
color_y	named list of the colors for y axis labels. Defualt is NULL.

Details

A data.frame created by inferGenotypeBaysian.

Value

The following list is returned:

• 'p': heat-map visualization of the genotype inference for multiple samples.

• 'width': Optimal width value for rendering plot.

• 'height': Optimal width value for rendering plot.

When a file is supplied the graph is also rendered directly to pdf.

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