plot_cnv: Plot the matrix as a heatmap, with cells as rows and genes as...
In infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data

Description Usage Arguments Value Examples

Formats the data and sends it for plotting.

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 = 3,
  contig_cex = 1,
  x.center = mean(infercnv_obj@expr.data),
  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
)

`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.
`useRaster`	Whether to use rasterization for drawing heatmap. Only disable if it produces an error as it is much faster than not using it.

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.

# 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
         )