Create and save a table with the functional enrichment analysis results.
This function creates a table mainly for the results from gost() function. However, if the input at least contains columns named 'term_id' and 'p_value' then any enrichment results data frame can be visualised in a table with this function.
publish_gosttable(
gostres,
highlight_terms = NULL,
use_colors = TRUE,
show_columns = c("source", "term_name", "term_size", "intersection_size"),
filename = NULL,
ggplot = TRUE
)gostres |
named list from gost() function (with names 'result' and 'meta') or a data frame that has columns named "term_id" and "p_value(s)". |
highlight_terms |
vector of selected term IDs from the analysis or a (subset) data.frame that has a column called 'term_id'. All data is shown if set to NULL. |
use_colors |
if enabled, the p-values are highlighted in the viridis colorscale just as in g:Profiler, otherwise the table has no background colors. |
show_columns |
names of additional columns to show besides term_id and p_value. By default the output table shows additional columns named "source", "term_name", "term_size", "intersection_size" |
filename |
file name to create on disk and save the annotated plot. Filename extension should be from c("png", "pdf", "jpeg", "tiff", "bmp"). |
ggplot |
if FALSE, then the function returns a gtable object. |
The output table is very similar to the one shown under the Manhattan plot.
The output is a ggplot object.
Liis Kolberg <liis.kolberg@ut.ee>
gostres <- gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
publish_gosttable(gostres, highlight_terms = c("GO:0001010", "REAC:R-MMU-8939245"))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.