plot_cnv: 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, k_obs_groups = 3, contig_cex = 1,
  x.center = 0, x.range = NA, hclust_method = "ward.D",
  color_safe_pal = TRUE, output_filename = "infercnv",
  output_format = "png", ref_contig = NULL, write_expr_matrix = FALSE)

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.

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.

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

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.

Value

No return, void.