heatmap_main: Draw a heatmap of processed data

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Draw a heatmap of processed data

Description

Uses the package ComplexHeatmaps to draw a heatmap of the processed data that has been prepared for the heatmap. The returned heatmap visualizes the processed expression of the gene range provided in process_heatmap_data().

Usage

heatmap_main(
  data,
  cluster_meth,
  heatmap_cutoff,
  sample_info,
  select_factors_heatmap,
  dist_funs,
  dist_function,
  hclust_function,
  sample_clustering,
  heatmap_color_select,
  row_dend,
  k_clusters,
  re_run,
  selected_genes
)

Arguments

data	Data matrix returned from process_heatmap_data()
cluster_meth	Integer indicating which clustering method to use 1 for hierarchical and 2 for kmeans.
heatmap_cutoff	Numeric value for Z score max to filter data
sample_info	Matrix of experiment design information from load data
select_factors_heatmap	Factor group for annotation legend
dist_funs	List of distance functions to use in heatmap
dist_function	The selected distance function to use
hclust_function	Type of clustering to perform
sample_clustering	TRUE/FALSE Specify whether to cluster columns
heatmap_color_select	Vector of colors for heatmap scale
row_dend	TRUE/FALSE Hide row dendrogram,
k_clusters	Number of clusters to use for k-means
re_run	Integer for a seed to Re-run k-means with
selected_genes	Character list of genes to label on the heatmap

Value

Heatmap of the processed data.

See Also

• dist_functions() for available distance functions,

• hcluster_functions() for available functions for hierarchical

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

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

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