process_heatmap_data: Heatmap data processing

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Heatmap data processing

Description

This function prepares the data from pre-processing to be displayed in a heatmap. It takes in limits for what genes to subset, what centering and standardizing to perform, and what gene ID label to use.

Usage

process_heatmap_data(
  data,
  n_genes_max,
  gene_centering,
  gene_normalize,
  sample_centering,
  sample_normalize,
  all_gene_names,
  select_gene_id
)

Arguments

data	Processed data matrix
n_genes_max	Integer for for number upper limit to display in heatmap
gene_centering	TRUE/FALSE subtract mean from gene rows
gene_normalize	TRUE/FALSE divide by SD in gene rows
sample_centering	TRUE/FALSE subtract mean from sample columns
sample_normalize	TRUE/FALSE divide by SD in sample columns
all_gene_names	Data frame of gene names
select_gene_id	Character string designating desired ID type for heatmap labels (User_ID, ensembl_ID, symbol)

Value

Subsetted data matrix ([n_genes_min:n_genes_max, ]) with gene IDs as the select_gene_id

See Also

Other clustering functions: cluster_heat_click_info(), draw_sample_tree(), heat_sub(), heatmap_main(), k_means_elbow(), sd_density(), sub_heat_ann()

Other heatmaps: cluster_heat_click_info(), heat_sub(), heatmap_main(), sub_heat_ann()

espors/idepGolem documentation built on Oct. 27, 2024, 4:56 a.m.