plot_heatmaps: Plots for the hit distribution of all genes

In arendsee/phylostratr: Analyze phylostratigraphic data

Plots for the hit distribution of all genes

Description

Plots for the hit distribution of all genes

Usage

plot_heatmaps(
  hits,
  filename,
  tree = NULL,
  n = 50,
  focal_id = NULL,
  to_name = TRUE,
  scheme = scheme2
)

Arguments

hits	A table of best hits
filename	Name of the output PDF file
tree	An optional phylo object, if it is not given, a tree will be infrerred from the taxon IDs in the 'staxid' column. This will work only if all these IDs are valid NCBI taxonomy IDs.
n	The number of genes to display per page
focal_id	The focal taxonomy ID (if given, this will be used to order the tree relative with the focal species on top)
to_name	If TRUE, then the tip labels will be converted from taxonomy IDs to scientific names
scheme	Color scheme

Examples

## Not run: 
plot_heatmaps(hits, "heatmaps.pdf", tree=strata@tree) 

# You can change the colorscheme and cutoffs:
funky_scheme <- list(
  cutoff = c(1e-20, 1e-5, 1e-3, 1), 
  color  = c('blue', 'green', 'yellow', 'darkorange1', 'darkred')
)
plot_heatmaps(hits, "heatmaps.pdf", tree=strata@tree, scheme=funky_scheme)

## End(Not run)

arendsee/phylostratr documentation built on Dec. 23, 2024, 1:31 p.m.