plot_cnv: Plot the matrix as a heatmap, with cells as rows and genes as...

In broadinstitute/infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data

Plot the matrix as a heatmap, with cells as rows and genes as columns, ordered according to chromosome

Description

Formats the data and sends it for plotting.

Usage

plot_cnv(
  infercnv_obj,
  out_dir = ".",
  title = "inferCNV",
  obs_title = "Observations (Cells)",
  ref_title = "References (Cells)",
  cluster_by_groups = TRUE,
  cluster_references = TRUE,
  plot_chr_scale = FALSE,
  chr_lengths = NULL,
  k_obs_groups = 1,
  contig_cex = 1,
  x.center = mean([e-mail]),
  x.range = "auto",
  hclust_method = "ward.D",
  custom_color_pal = NULL,
  color_safe_pal = FALSE,
  output_filename = "infercnv",
  output_format = "png",
  png_res = 300,
  dynamic_resize = 0,
  ref_contig = NULL,
  write_expr_matrix = FALSE,
  write_phylo = FALSE,
  useRaster = TRUE
)

Arguments

infercnv_obj	infercnv object
out_dir	Directory in which to save pdf and other output.
title	Plot title.
obs_title	Title for the observations matrix.
ref_title	Title for the reference matrix.
cluster_by_groups	Whether to cluster observations by their annotations or not. Using this ignores k_obs_groups.
cluster_references	Whether to cluster references within their annotations or not. (dendrogram not displayed)
plot_chr_scale	Whether to scale the chromosme width on the heatmap based on their actual size rather than just the number of expressed genes.
chr_lengths	A named list of chromsomes lengths to use when plot_chr_scale=TRUE, or else chromosome size is assumed to be the last chromosome's stop position + 10k bp
k_obs_groups	Number of groups to break observation into.
contig_cex	Contig text size.
x.center	Value on which to center expression.
x.range	vector containing the extreme values in the heatmap (ie. c(-3,4) )
hclust_method	Clustering method to use for hclust.
custom_color_pal	Specify a custom set of colors for the heatmap. Has to be in the shape color.palette(c("darkblue", "white", "darkred"), c(2, 2))
color_safe_pal	Logical indication of using a color blindness safe palette.
output_filename	Filename to save the figure to.
output_format	format for heatmap image file (default: 'png'), options('png', 'pdf', NA) If set to NA, will print graphics natively
png_res	Resolution for png output.
dynamic_resize	Factor (>= 0) by which to scale the dynamic resize of the observation heatmap and the overall plot based on how many cells there are. Default is 0, which disables the scaling. Try 1 first if you want to enable.
ref_contig	If given, will focus cluster on only genes in this contig.
write_expr_matrix	Includes writing a matrix file containing the expression data that is plotted in the heatmap.
write_phylo	Write newick strings of the dendrograms displayed on the left side of the heatmap to file.
useRaster	Whether to use rasterization for drawing heatmap. Only disable if it produces an error as it is much faster than not using it.

Value

A list of all relevent settings used for the plotting to be able to reuse them in another plot call while keeping consistant plotting settings, most importantly x.range.

Examples

# data(infercnv_data_example)
# data(infercnv_annots_example)
# data(infercnv_genes_example)

# infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, 
#                                                           gene_order_file=infercnv_genes_example,
#                                                           annotations_file=infercnv_annots_example,
#                                                           ref_group_names=c("normal"))

# infercnv_object_example <- infercnv::run(infercnv_object_example,
#                                          cutoff=1,
#                                          out_dir=tempfile(), 
#                                          cluster_by_groups=TRUE, 
#                                          denoise=TRUE,
#                                          HMM=FALSE,
#                                          num_threads=2,
#                                          no_plot=TRUE)

data(infercnv_object_example)

plot_cnv(infercnv_object_example,
         out_dir=tempfile(),
         obs_title="Observations (Cells)",
         ref_title="References (Cells)",
         cluster_by_groups=TRUE,
         x.center=1,
         x.range="auto",
         hclust_method='ward.D',
         color_safe_pal=FALSE,
         output_filename="infercnv",
         output_format="png",
         png_res=300,
         dynamic_resize=0
         )

broadinstitute/infercnv documentation built on Dec. 3, 2023, 6:58 p.m.