olink_pathway_heatmap: Creates a heatmap of selected pathways and proteins

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

Creates a heatmap of selected pathways and proteins

Description

Creates a heatmap of proteins related to pathways using enrichment results from olink_pathway_enrichment.

Usage

olink_pathway_heatmap(
  enrich_results,
  test_results,
  method = "GSEA",
  keyword = NULL,
  number_of_terms = 20
)

Arguments

enrich_results	data frame of enrichment results from olink_pathway_enrichment()
test_results	filtered results from statistical test with Assay, OlinkID, and estimate columns
method	method used in olink_pathway_enrichment ("GSEA" (default) or "ORA")
keyword	(optional) keyword to filter enrichment results on, if not specified, displays top terms
number_of_terms	number of terms to display, default is 20

Value

A heatmap as a ggplot object

See Also

• olink_pathway_enrichment for generating enrichment results

• olink_pathway_visualization for generating a bar graph of results

Examples

library(dplyr)
# Run t-test results (see olink_ttest documentation)
npx_df <- npx_data1 %>% filter(!grepl('control',SampleID, ignore.case = TRUE))
ttest_results <- olink_ttest(df=npx_df,
                             variable = 'Treatment',
                            alternative = 'two.sided')

try({ # This expression might fail if dependencies are not installed
#  Run olink_pathway_enrichment (see documentation)
gsea_results <- olink_pathway_enrichment(data = npx_data1, test_results = ttest_results)
ora_results <- olink_pathway_enrichment(data = npx_data1,
                                        test_results = ttest_results, method = "ORA")
olink_pathway_heatmap(enrich_results = gsea_results, test_results = ttest_results)
olink_pathway_heatmap(enrich_results = ora_results, test_results = ttest_results,
                      method = "ORA", keyword = "cell")
})

OlinkAnalyze documentation built on Nov. 4, 2023, 1:07 a.m.