rabhit (version 0.2.5)

hapHeatmap: Graphical output of alleles division by chromosome

Description

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

Usage

hapHeatmap(
  hap_table,
  chain = c("IGH", "IGK", "IGL", "TRB", "TRA"),
  genes_order = NULL,
  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
)

Value

A list with the following:

• 'p': heat-map visualization of the haplotype 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 to pdf.

Arguments

hap_table

haplotype summary table. See details.

chain

the IG chain: IGH,IGK,IGL. Default is IGH.

genes_order

A vector of the genes by the desired order. Default is by GENE.loc

removeIGH

if TRUE, 'IGH'\'IGK'\'IGL'\'TRB' prefix is removed from gene names.

lk_cutoff

the lK cutoff value to be considered low for texture layer. Default is lK<1.

mark_low_lk

if TRUE, a texture is add for low lK values. Default is TRUE.

size_annot

size of bottom annotation text. Default is 1.5 .

color_y

named list of the colors for y axis labels.

order_subject

order subject by a vector.

file

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

size_text

text size for annotations.

ylabel_size

text size for y axis labels.

Details

A data.frame created by createFullHaplotype.

Examples

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