kegg_pathway: Use KEGG to create a pathway diagram

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Use KEGG to create a pathway diagram

Description

In the database, use the KEGG information to create an image that is a diagram of the pathway that is being enriched.

Usage

kegg_pathway(
  go,
  gage_pathway_data,
  sig_pathways,
  select_contrast,
  limma,
  converted,
  idep_data,
  select_org,
  low_color = "green",
  high_color = "red"
)

Arguments

go	String designating the section of the database to query for pathway analysis. See gmt_category() for choices.
gage_pathway_data	Matrix returned from gage_data()
sig_pathways	Description of the pathway for which to obtain the gene expression data
select_contrast	String designating the comparison from DEG analysis to filter for the significant genes. See the 'comparison' element from the list returned from limma_value() for options.
limma	Results list from limma_value()
converted	Return value from the convert_id(), contains information about the gene IDs for the matched species
idep_data	Read data files from get_idep_data()
select_org	The organism that the gene data is for
low_color	String designating color value for the low-ly expressed genes
high_color	String designating color value for the high-ly expressed genes

Value

Make an image and return the path to the image to be rendered in the server.

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(), pathway_select_data(), pgsea_data(), pgsea_plot_all(), plot_gsva(), plot_pgsea(), reactome_data(), remove_pathway_id(), remove_pathway_id_second()

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