olink_pathway_visualization {OlinkAnalyze}

Creates bargraph of top/selected enrichment terms from GSEA or ORA results from olink_pathway_enrichment()

Description

Pathways are ordered by increasing p-value (unadjusted)

Usage

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

Arguments

enrich_results

data frame of enrichment results from olink_pathway_enrichment()

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 bargraph as a ggplot object

See Also

• olink_pathway_enrichment for generating enrichment results

• olink_pathway_heatmap for generating a heat map of results

Examples

library(dplyr)
# Run olink_ttest or other stats test (see documentaiton )
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_visualization(enrich_results = gsea_results)
olink_pathway_visualization(enrich_results = gsea_results, keyword = "immune")
olink_pathway_visualization(enrich_results = ora_results, method = "ORA", number_of_terms = 15)
})