plot_involved_miRNAs_to_modules: plots the heatmap of miRNAs invovled in the interactions of...

In biomedbigdata/SPONGE: Sparse Partial Correlations On Gene Expression

plots the heatmap of miRNAs invovled in the interactions of the modules (see Boniolo and Hoffmann 2022 et al. Fig. 7a)

Description

plots the heatmap of miRNAs invovled in the interactions of the modules (see Boniolo and Hoffmann 2022 et al. Fig. 7a)

Usage

plot_involved_miRNAs_to_modules(
  sponge_modules,
  trained_model,
  gene_mirna_candidates,
  k_modules = 25,
  filter_miRNAs = 3,
  bioMart_gene_symbol_columns = "hgnc_symbol",
  bioMart_gene_ensembl = "hsapiens_gene_ensembl",
  width = 5,
  length = 5,
  show_row_names = T,
  show_column_names = T,
  show_annotation_column = F,
  title = "Frequency",
  legend_height = 1.5,
  labels_gp_fontsize = 8,
  title_gp_fontsize = 8,
  legend_width = 3,
  column_title = "Module",
  row_title = "miRNA",
  row_title_gp_fontsize = 10,
  column_title_gp_fontsize = 10,
  row_names_gp_fontsize = 7,
  column_names_gp_fontsize = 7,
  column_names_rot = 45,
  unit = "cm"
)

Arguments

sponge_modules	result of define_modules()
trained_model	returned from train_and_test_model
gene_mirna_candidates	output of SPONGE or SPONGEdb (miRNAs_significance)
k_modules	top k modules to be shown (default: 25)
filter_miRNAs	min rowsum to be reach of miRNAs (default: 3.0)
bioMart_gene_symbol_columns	bioMart dataset column for gene symbols (e.g. human: hgnc_symbol, mouse: mgi_symbol) (default: hgnc_symbol)
bioMart_gene_ensembl	bioMart gene ensemble name (e.g., hsapiens_gene_ensembl)
width	the width of the heatmap (default: 5)
length	the length of the heatmap (default: 5)
show_row_names	show row names (default: T)
show_column_names	show column names (default: T)
show_annotation_column	add annotation column to columns (default: F)
title	the title of the plot (default: "Frequency")
legend_height	the height of the legend (default: 1.5)
labels_gp_fontsize	the font size of the labels (default: 8)
title_gp_fontsize	the font size of the title (default: 8)
legend_width	the width of the legend (default: 3)
column_title	the column title (default: "Module")
row_title	the title of the rows (default: "miRNA")
row_title_gp_fontsize	the font size of the row title (default: 10)
column_title_gp_fontsize	the font size of the column title (default: 10)
row_names_gp_fontsize	the font size of the row names (default: 7)
column_names_gp_fontsize	the font size of the column names (default: 7)
column_names_rot	the rotation angel of the column names (default: 45)
unit	either cm or inch (see ComplexHeatmap parameter)

Value

plot object

biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.