infercnv (version 1.3.3)

plot_per_group: plot_per_group

Description

Takes an infercnv object and subdivides it into one object per group of cells to allow plotting of each group on a seperate plot. If references are selected, they will appear on the observation heatmap area as it is larger.

Usage

plot_per_group(infercnv_obj, on_references = TRUE,
  on_observations = TRUE, sample = FALSE, n_cells = 1000,
  every_n = NULL, above_m = 1000,
  base_filename = "infercnv_per_group", output_format = "png",
  write_expr_matrix = TRUE, save_objects = FALSE, png_res = 300,
  dynamic_resize = 0, out_dir)

Arguments

infercnv_obj

infercnv_object

on_references

boolean (default=TRUE), plot references (normal cells).

on_observations

boolean (default=TRUE), plot observations data (tumor cells).

sample

Whether unique groups of cells should be sampled from or not. (see other parameters for how sampling is done) (Default: FALSE)

n_cells

Number of cells that should be sampled per group if sampling is enabled (default = 1000) .

every_n

Sample 1 cell every_n cells for each group that has above_m cells, if sampling is enabled. If subclusters are defined, this will make sure that at least one cell per subcluster is sampled. Requires above_m to be set to work, overriding n_cells parameter. (Default: NULL)

above_m

Sample only groups that have at least above_m cells if sampling is enabled. (default: 1000) Does not require every_n to be set.

base_filename

Base prefix for the output files names. Will be followed by OBS/REF to indidate the type of the group, and the group name. (Default: "infercnv_per_group")

output_format

Output format for the figure. Choose between "png", "pdf" and NA. NA means to only write the text outputs without generating the figure itself. (default: "png")

write_expr_matrix

Includes writing a matrix file containing the expression data that is plotted in the heatmap. (default: FALSE)

save_objects

Whether to save the infercnv objects generated for each group as RDS. (default: FALSE)

png_res

Resolution for png output. (Default: 300)

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. (Default: 0)

out_dir

Directory in which to save plots and other outputs.

Value

void

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)

infercnv::plot_per_group(infercnv_obj, out_dir=tempfile())

# }