| plot_fulltaxo {metaprotr} | R Documentation |
plot_fulltaxo
Description
Provides the number of taxonomic entities per sample in the different taxonomic levels. The taxonomic levels are: species, genus, family, order, class, phylum and superkingdom.
Usage
plot_fulltaxo(spectral_count_object, force = FALSE)
Arguments
spectral_count_object |
List defined as "spectral_count_object" containing dataframes with format similar to that generated with the function "getsc_specific". This object contains abundances expressed as spectral counts from peptides, subgroups (metaproteins) or groups. Taxonomy must have previously been added with the function "add_taxonomy". |
force |
Logic value set at FALSE by default in order to ask permission to create a pdf and a csv file in the workstation of the user. |
Value
Bar plots (pdf) and csv file with the number of taxonomic species, genus, family, order, class, phylum and superkingdom per sample. An additional csv file is generated providing the rate of assignment. The rate of assigment corresponds to the ratio between the number of the most frequent annotation ("species", "genus", "family", "order", "class", "phylum" or "superkingdom") and the total number of elements within each level of the spectral category under study (subgroup or group). The csv file is generated only when the "spectral_count_object" is organized by subgroup or by group.
Examples
data(fecal_waters)
plot_fulltaxo(fecal_waters)