do_CNVHeatmap() | Copy number variation

CNV heatmaps display chromosomal copy number variations across cells using output from inferCNV. Shows CNV scores aggregated by chromosome or chromosome arm across cell populations.

Plots will be released at a later time!

Basic usage

First run inferCNV:

# Load chromosome locations
data("human_chr_locations", package = "SCpubr")

p <- SCpubr::do_CNVHeatmap(sample = sample,
                           infercnv_object = infercnv_obj,
                           chromosome_locations = human_chr_locations)
p

Include chromosome arms

p <- SCpubr::do_CNVHeatmap(sample = sample,
                           infercnv_object = infercnv_obj,
                           chromosome_locations = human_chr_locations,
                           include_chr_arms = TRUE)
p

Show values

p <- SCpubr::do_CNVHeatmap(sample = sample,
                           infercnv_object = infercnv_obj,
                           chromosome_locations = human_chr_locations,
                           values.show = TRUE)
p

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling, grid), see Shared features.

Core parameters

Parameter Description Default
infercnv_object Output from inferCNV —
chromosome_locations Chromosome region data —
include_chr_arms Show p/q arms FALSE
return_object Return data along with plot FALSE

Metacells

Parameter Description Default
using_metacells inferCNV used metacells FALSE
metacell_mapping Cell-metacell mapping NULL

Values display

Parameter Description Default
values.show Show numeric values FALSE
values.size Value text size 3
values.threshold Only show above threshold NULL
values.round Decimal places 1

See also