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Plot over-representation analysis results

Source: R/enrichment_analysis.R
hd_plot_ora.Rd

hd_plot_ora() generates useful visualizations for the results of the over-representation analysis.

Usage

hd_plot_ora(enrichment, seed = 123)

Arguments

enrichment

The enrichment results obtained from hd_ora().

seed

Seed for reproducibility. Default is 123.

Value

The input object enriched with the plots.

Details

When KEGG database is used, a cnetplot is generated with ENTREZIDs instead of gene names. For GO and Reactome databases the ENTREZIDs are converted to gene names. If you get the "grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), : Viewport has zero dimension(s)" warning or error, try to increase the RStudio's viewer window size.

Examples

# Initialize an HDAnalyzeR object
hd_object <- hd_initialize(example_data, example_metadata)

# Run differential expression analysis for AML vs all others
de_results <- hd_de_limma(hd_object, case = "AML")

# Extract the up-regulated proteins for AML
sig_up_proteins_aml <- de_results$de_res |>
  dplyr::filter(adj.P.Val < 0.05 & logFC > 0.5) |>
  dplyr::pull(Feature)

# Perform ORA with `GO` database and `BP` ontology
enrichment <- hd_ora(sig_up_proteins_aml, database = "GO", ontology = "BP")
#> No background gene list provided. For meaningful enrichment results, it is recommended to specify a relevant background list of genes (e.g., the full proteome or a set of genes that could be impacted in your experiment). The absence of a background may lead to misleading results in the over-representation analysis (ORA).
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: coercing argument of type 'double' to logical

# Plot the results
enrichment <- hd_plot_ora(enrichment)
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.

# Access the plots
enrichment$dotplot

enrichment$treeplot

enrichment$cnetplot