Function to plot functional relevance results

Graphical function to plot (relative) functional relevance results.

Usage

plot_functional_relevance(
  fr,
  method = "count",
  file_name = NULL,
  plot_names = T,
  pal = NULL,
  jitter_width = 0.07,
  jitter_height = 0.07,
  width = 200,
  height = 200,
  res = 300,
  units = "mm"
)

Arguments

fr

the data.frame obtained as `gene_functional_relevance()` result

method

= c("count", "relative") If "count" then the functional and interactor diversity and functional relevance are used, otherwise the relative ones

file_name

file name of the plot, if `NULL` the plot will be returned by the function

plot_names

logical, or a vector with the same length and order of the genes in `fr`. If `TRUE` all genes name are plotted, if `FALSE` no names are plotted, otherwise the passed vector is used to label genes and all of them are plotted

pal

vector of three color to be used to create the gradient to color the genes according to (relative) functional relevance score. If `NULL` the Brewer "Spectral" palette is used

jitter_width, jitter_height

values to control point jitter in the plot. See ggplot2::geom_jitter() for details

width, height, res, units

values used to save the plot in jpeg format, see grDevices::jpeg() for details

Value

If `file_name` The function returns the ggplot object

Details

The function plots (relative) functional relevance results obtained with `gene_functional_relevance()` function. Each gene is plotted by interactor and functional diversity, and is colored by functional relevance score