gprofiler2: publish_gostplot – R documentation

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publish_gostplot

Create and save an annotated Manhattan plot of enrichment results.

Description

This function allows to highlight a list of selected terms on the Manhattan plot created with the gprofiler2::gostplot() function. The resulting plot is saved to a publication ready image if 'filename' is specified. The plot is very similar to the one shown in the g:GOSt web tool after clicking on circles.

Usage

publish_gostplot(
  p,
  highlight_terms = NULL,
  filename = NULL,
  width = NA,
  height = NA
)

Arguments

`p`	ggplot object from gostplot(gostres, interactive = FALSE) function
`highlight_terms`	vector of selected term IDs from the analysis or a (subset) data.frame that has a column called 'term_id'. No annotation is added if set to NULL.
`filename`	file name to create on disk and save the annotated plot. Filename extension should be from c("png", "pdf", "jpeg", "tiff", "bmp").
`width`	plot width in inches. If not supplied, the size of current graphics device is used.
`height`	plot height in inches. If not supplied, the size of current graphics device is used.

Value

The output is a ggplot object.

Author(s)

Liis Kolberg <liis.kolberg@ut.ee>

Examples

gostres <- gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
 p <- gostplot(gostres, interactive = FALSE)
 publish_gostplot(p, highlight_terms = c("GO:0001010", "REAC:R-MMU-8939245"))

gprofiler2

Interface to the 'g:Profiler' Toolset

v0.2.0

GPL (>= 2)

Authors

Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>

Initial release