metaprotr (version 1.2.2)

plot_stackedtaxo: plot_stackedtaxo

Description

Generates stacked barplots of the spectral counts distributions among the different taxonomic entities ("species", "genus", "family", "order", "class", "phylum" or "superkingdom") within the samples or conditions of a "spectral_count_object" with taxonomy. If the provided conditions have several replicates the mean value is taken into account.

Usage

plot_stackedtaxo(
  spectral_count_object,
  target_variable,
  bars_data,
  filter_percent = 1,
  force = FALSE
)

Arguments

spectral_count_object

List defined as "spectral_count_object" containing dataframes with spectral counts abundance organized by taxonomy (species, genus, family, order, class, phylum or superkingdom). This object is generated with the function "crumble_taxonomy".

target_variable

Character indicating the name of one column from metadata. The stacked barplots will be ordered by the levels of this variable.

bars_data

Character indicating the type of labels to be displayed in the stacked bars. The possible options are "percent" or "numbers".

filter_percent

Optional numeric value between 0 and 99 that sets the minimal percentage of spectral counts at which the taxonomic elements will be displayed. The elements whose values are lower than this number will be gathered and displayed as "others". The default value is set at 1.

force

Logic value set at FALSE by default in order to ask permission to create a pdf in the workstation of the user.

Value

Barplots (pdf) of the taxonomic distribution of the samples present in a "spectral_count_object" with taxonomic levels.

Examples

# NOT RUN {
data(species_fw)

plot_stackedtaxo(species_fw, 'SampleID', 'percent', 2)

plot_stackedtaxo(species_fw, 'SC_name', 'numbers')

# }