metaprotr (version 1.2.2)

plot_intensities: plot_intensities

Description

Draws violin plots containing the abundance intensities expressed as spectral counts per level (peptides, subgroups, groups or taxonomic entities) in provided samples or conditions from a "spectral_count_object". If the provided conditions have several replicates the mean value is taken into account.

Usage

plot_intensities(
  spectral_count_object,
  target_variable,
  image_title = NULL,
  force = FALSE
)

Arguments

spectral_count_object

List defined as "spectral_count_object" containing dataframes with abundance expressed as spectral counts from peptides, subgroups, groups or taxonomic levels. The format of this object is similar to that generated from the functions "getsc_specific" and "crumble_taxonomy".

target_variable

Character indicating the name of one column from metadata, the column must contain the conditions to be displayed.

image_title

Character indicating the title to be displayed in the generated image.

force

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

Value

Violin plots (pdf) indicating the spectral counts of the different levels (peptides, subgroups, groups or taxonomic entities) per sample or condition.

Examples

# NOT RUN {
data(fecal_waters)
plot_intensities(fecal_waters, "SC_name", "Title to display inside the plot")

data(species_fw)
plot_intensities(species_fw, "Condition", "Abundance per condition")

# }