Bubble plot of enrichment values

plot_enrichment() is a GGplot2 implementation for plotting the enrichment values. This function can take either a tidyproteomics data object or a table with the required headers.

Usage

plot_enrichment(
  data = NULL,
  ...,
  .term = NULL,
  enrichment_min = 1,
  enrichment_column = "enrichment",
  significance_max = 0.01,
  significance_column = "p_value",
  term_column = "annotation",
  size_column = "size",
  destination = "plot",
  height = 5,
  width = 8
)

Arguments

data

a tidyproteomics data object

...

two sample comparison

.term

a character string indicating the term enrichment analysis should be calculated for

enrichment_min

a numeric defining the minimum log2 enrichment to highlight.

enrichment_column

a character defining the column name of enrichment values.

significance_max

a numeric defining the maximum statistical significance to highlight.

significance_column

a character defining the column name of the statistical significance values.

term_column

a character defining the column name for labeling.

size_column

a character defining the column name of term size.

destination

a character string

height

a numeric

width

a numeric

Value

a ggplot2 object

Examples

library(dplyr, warn.conflicts = FALSE)
library(ggplot2, warn.conflicts = FALSE)
library(tidyproteomics)
hela_proteins %>%
   expression(knockdown/control, .method = stats::t.test) %>%
   enrichment(knockdown/control, .terms = 'biological_process', .method = "wilcoxon") %>%
   plot_enrichment(knockdown/control, .term = "biological_process") +
   labs(title = "Hela: Term Enrichment", subtitle = "Knockdown ~ Control")
#> ℹ .. expression::t_test testing knockdown / control
#> ✔ .. expression::t_test testing knockdown / control [3.2s]
#> 
#> ℹ .. enrichment::wilcoxon testing knockdown / control by term biological_process
#> ℹ annotation other had issues, not reported
#> ℹ .. enrichment::wilcoxon testing knockdown / control by term biological_process

#> ✔ .. enrichment::wilcoxon testing knockdown / control by term biological_proces…
#>