DEET_enrichment_plot {DEET}

DEET_enrichment_plot

Description

Generate barplots or dotplots from the output of DEET

Usage

DEET_enrichment_plot(
  enrich_list,
  outname,
  width = 8,
  text_angle = 0,
  horizontal = FALSE,
  topn = 5,
  ol_size = 1,
  exclude_domain = "",
  cluster_order = NULL,
  dot = FALSE,
  colors = "Set2",
  split_domain = FALSE
)

Arguments

enrich_list

A list of enrichments from DEET, with each element post-processed with the barplot enrichment function.

outname

A character giving the title of the barplot or dotplot.

width

The number of inches in the barplot or dotplot.

text_angle

The angle of the enriched studies.

horizontal

Whether the output barplot is vertical or horizontal

topn

the top number of studies (by p-value) to be plotted.

ol_size

the minimum number of overlapping genes (or paths) in an enriched study.

exclude_domain

Exclude studies enriched based on DEGs, Paths, or TF if the user happened to aggregate the results into a single DF, generally unused.

cluster_order

Factor to group studies based on the researchers custom annotation.

dot

logical (T/F) of whether to produce a dotplot or a barplot

colors

Type of color pallete to input into 'scale_fill_brewer' of ggplot.

split_domain

logical (T/F) of whether to plot the "topn" studies for each "domain" (default is source) or to plot the topn pathwys regardless of domain. default is set to FALSE, meaning it plots the topn pathways regardless of domain.

Value

A ggplot2 object (barplot or dotplot) of enrichment identified within DEET.

Author(s)

Dustin Sokolowski, Hauyun Hou PhD

Examples

data("example_DEET_enrich_input")
data("DEET_example_data")
DEET_out <- DEET_enrich(example_DEET_enrich_input, DEET_dataset = DEET_example_data)

# converting output to format compatible with DEET_enrichment plot
DE_example <- DEET_out$AP_DEET_DE_output$results
DE_example$term.name <- DEET_out$AP_DEET_DE_output$metadata$DEET.Name
DE_example$domain <- "DE"
DE_example$overlap.size <- lengths(DE_example$overlap)
DE_example$p.value <- DE_example$adjusted_p_val

DE_example_plot <- DEET_enrichment_plot(list(DE_example = DE_example), "DE_example")