infercnv (version 1.3.3)

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, cluster_references = TRUE,
  k_obs_groups = 3, 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, 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)

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.

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

# NOT RUN {
# data(data)
# data(annots)
# data(genes)

# infercnv_obj <- infercnv::CreateInfercnvObject(raw_counts_matrix=data, 
#                                                gene_order_file=genes,
#                                                annotations_file=annots,
#                                                ref_group_names=c("normal"))

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

data(infercnv_object)

plot_cnv(infercnv_obj,
         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
         )

# }