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

View source: R/fn_spongeffects_utility.R

plot_involved_miRNAs_to_modulesR Documentation

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.