hapHeatmap: Graphical output of alleles division by chromosome

Description Usage Arguments Details Value Examples

View source: R/graphic_functions.R

Description

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

Usage

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hapHeatmap(
  hap_table,
  chain = c("IGH", "IGK", "IGL"),
  gene_sort = "position",
  removeIGH = TRUE,
  lk_cutoff = 1,
  mark_low_lk = TRUE,
  size_annot = 1.5,
  color_y = NULL,
  order_subject = NULL,
  file = NULL,
  size_text = NULL,
  ylabel_size = 1
)

Arguments

hap_table

haplotype 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.

size_annot

size of bottom annotation text. Defualt is 1.5 .

color_y

named list of the colors for y axis labels.

order_subject

order subject by a vecor.

file

file path for rendering the plot to pdf. If non is supplied than the plot is retured as object. Defualt is NULL.

size_text

text size for annotations.

ylabel_size

text size for y axis labels.

Details

A data.frame created by createFullHaplotype.

Value

A list with the following:

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

Examples

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# Plotting haplotpe heatmap
p <- hapHeatmap(samplesHaplotype)
p$p

Example output

Loading required package: ggplot2
RAbHIT version: 0.1.5

rabhit documentation built on July 12, 2020, 1:06 a.m.