View source: R/graphic_functions.R
hapHeatmap | R Documentation |
The hapHeatmap
function generates a graphical output of the alleles per gene in multiple samples.
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 )
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. |
A data.frame
created by createFullHaplotype
.
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.
# Plotting haplotpe heatmap p <- hapHeatmap(samplesHaplotype) p$p
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