rba_string_enrichment_image {rbioapi}R Documentation

Get STRING Enrichment Plot

Description

In addition to performing enrichment analysis, STRING allows you to also visualize the analysis results. Use rba_string_enrichment to retrieve the analysis results as a data frame.

Usage

rba_string_enrichment_image(
  ids,
  species,
  category = "Process",
  image_format = "image",
  save_image = TRUE,
  group_by_similarity = NULL,
  color_palette = "mint_blue",
  number_of_term_shown = 10,
  x_axis = "signal",
  ...
)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information. Note that if only one id is supplied, STRING expands the network by 10 proteins.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606.

category

The terms set to use to perform enrichment analysis. valid values are (See details for more info): "Process" (default), "Function", "Component", "Keyword", "KEGG", "RCTM", "HPO", "MPO", "DPO", "WPO", "ZPO", "FYPO", "Pfam", "SMART", "InterPro", "PMID", "NetworkNeighborAL", "COMPARTMENTS", "TISSUES", "DISEASES", or "WikiPathways"

image_format

one of:

  • "image": PNG image with normal resolution.

  • "highres_image": High-resolution PNG image.

  • "svg": Scalable Vector Graphics image.

save_image

Logical or Character:

  • TRUE: Save the image to an automatically-generated path.

  • FALSE: Do not save the image, just return it as an R object.

  • Character string: A valid file path to save the image to.

group_by_similarity

Jackard index treshold to visually group the related terms. Valid values are between 0.1 to 1 with increment of 0.1. Default value is NULL (i.e. no grouping).

color_palette

Color pallet to code FDR values. Valid values are: "mint_blue" (default), "lime_emerald", "green_blue", "peach_purple", "straw_navy", or "yellow_pink"

number_of_term_shown

(default: 10) Maximum number of results to include in the plot.

x_axis

The variable to show on the x axis and rank the results based on it. Valid values are: "signal" (default), "strength", "FDR", or "gene_count"

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Details

Available values for category are as follow. Default value is "Process".

Value

A plot summarizing the enrichment results, which can be PNG or SVG depending on the inputs.

Corresponding API Resources

"POST https://string-db.org/api/{output_format}/enrichmentfigure"

References

See Also

rba_string_map_ids, rba_string_enrichment, rba_string_annotations

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_ppi(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Other "Enrichment/Over-representation": rba_enrichr(), rba_mieaa_enrich(), rba_panther_enrich(), rba_reactome_analysis(), rba_string_enrichment()

Examples

## Not run: 
  rba_string_enrichment_image(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606,
  category = "KEGG"
  )

## End(Not run)
## Not run: 
  rba_string_enrichment_image(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606,
  x_axis = "strength",
  number_of_term_shown = 20
  )

## End(Not run)
## Not run: 
  rba_string_enrichment_image(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606,
  color_palette = "straw_navy"
  )

## End(Not run)


[Package rbioapi version 0.8.2 Index]