plot_per_group {infercnv} | R Documentation |
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.
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)
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. |
void
# 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())