Generate data for ternary plot

Generate a three column matrix which can be used to draw a ternary plot.

generate_data_for_ternary(
  data_exp_mat = NULL,
  anno_signature_genes = NULL,
  gene_name_col = "GeneID",
  gene_type_col = "gene_type",
  weight_by_gene_count = TRUE,
  print_gene_num = FALSE,
  cutoff_exp = 0,
  prior_count = 2
)

Arguments

data_exp_mat

An expression matrix, e.g., raw count matrix or log2CPM matrix

anno_signature_genes

A data.frame containing signature gene annotation

gene_name_col

Colname name of row (gene) names used in the expression matrix

gene_type_col

Colname name of signature gene type annotation

weight_by_gene_count

Whether to divide the signature gene number by the total signature gene name, default is TRUE

print_gene_num

Print the signature gene number or not

cutoff_exp

Expression cut-offs used to count the signature gene number

prior_count

Add a prior count to avoid signature gene number to be 0, default is 2 but can be set to a different one

Examples

library(scTernary)

# Generate data for ternary plots
# using a CPM matrix and a CPM cut-off of 100

data_for_ternary <- generate_data_for_ternary(
  data_exp_mat = edgeR::cpm(example_dge_data$counts,
                            log = FALSE),
  anno_signature_genes = anno_signature_genes_mouse,
  gene_name_col = "GeneID",
  gene_type_col = "gene_type",
  weight_by_gene_count = FALSE,
  cutoff_exp = 100,
  prior_count = 0
)

vcdTernaryPlot(data = data_for_ternary,
  order_colnames = c(2,3,1),
  group = example_dge_data$samples$group,
  group_color = c("red","green","blue"),
  point_size = 1,
  legend_point_size = 0.6,
  legend_position = c(0.3,0.5),
  scale_legend = 1)