proccess_and_plot_DEET_enrich {DEET}

proccess_and_plot_DEET_enrich

Description

Generates barplots and dotplots based on the output of the DEET_enrich function.

Usage

proccess_and_plot_DEET_enrich(
  DEET_output,
  colour_barplot = "Source",
  width = 8,
  text_angle = 0,
  horizontal = F,
  topn = 5,
  ol_size = 1,
  exclude_domain = "",
  cluster_order = NULL,
  colors = "Set2"
)

Arguments

DEET_output

Direct output of the DEET_enrich function. A list with all of the same names as DEET_output.

colour_barplot

Pick dotplot or barplot colours. It can be NULL, in which all bars are the same or it can be a (case sensitive) column within the metadata. Defaults to "source".

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.

colors

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

Value

Named list where each element is a ggplot object plotting the output of the enrichment tests within DEET. The final element is the output of ActivePathways (in DEET) that is directly compatible with the DEET_enrichment_barplot function.

• DEET_DotPlot - ggplot object of Dotplot of enrichment of enrichment of DEET studies based on DE, BP, and TF information. Only plotted if 2/3 levels contain at least one significant study.

• Pathway_barplot - ggplot object of Barplot of standard gene set enrichment based on gene ontology and TFs. Only plotted if there is at least one enriched significant pathway/TF.

• individual_barplot - ggplot object of Barplot of the top enriched pathways or studies (depending on the input list).Barplot is only generated if each list has at least one pathway (or study) is enriched.

• DEET_output_forplotting - output of Activepathways with "domain", "overlap.size", and "p.value" columns added to be compatible with the DEET_enrichment_barplot function.

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)
plotting_example <- proccess_and_plot_DEET_enrich(DEET_out, text_angle = 45,
horizontal = TRUE, topn=4)