plot_gsva: Heatmap of GSVA pathway analysis

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Heatmap of GSVA pathway analysis

Description

Create a heatmap from the pathway analysis using the GSVA package. The heatmap shows the expression in each group for each significantly enriched pathway.

Usage

plot_gsva(
  my_range,
  processed_data,
  contrast_samples,
  gene_sets,
  pathway_p_val_cutoff,
  n_pathway_show,
  select_go,
  show_pathway_id,
  algorithm = "gsva"
)

Arguments

my_range	Vector of the (min_set_size, max_set_size)
processed_data	Matrix of gene data that has been through pre_process()
contrast_samples	Sample columns that correspond to the selected comparison
gene_sets	List of vectors with each vector being the set of genes that correspond to a particular pathway in the database. See list returned from read_gene_sets()
pathway_p_val_cutoff	Significant p-value to determine enriched pathways
n_pathway_show	Number of significant pathways to show
select_go	pathway category.
show_pathway_id	Whether to show pathway id for GO and KEGG pathways

Value

A heatmap plot with the rows as the significant pathways and the columns corresponding to the samples.

See Also

Other pathway functions: fgsea_data(), find_overlap(), gage_data(), get_gsva_plot_data(), get_pathway_list_data(), get_pgsea_plot_all_samples_data(), get_pgsea_plot_data(), gsva_data(), kegg_pathway(), pathway_select_data(), pgsea_data(), pgsea_plot_all(), plot_pgsea(), reactome_data(), remove_pathway_id(), remove_pathway_id_second()

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