plot_heatmaps | R Documentation |
Plots for the hit distribution of all genes
plot_heatmaps( hits, filename, tree = NULL, n = 50, focal_id = NULL, to_name = TRUE, scheme = scheme2 )
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 |
## 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)
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