plot_intensities_ratio: plot_intensities_ratio

In metaprotr: Metaproteomics Post-Processing Analysis

Description

Generates a scatter plot of the log2 (ratio + 1) between two conditions considering the spectral counts of each entity (peptides, subgroups, groups or taxonomic levels) from a "spectral_count_object". If a given condition has several replicates the mean value is taken into account.

Usage

plot_intensities_ratio(
  spectral_count_object,
  target_variable,
  list_conditions,
  force = FALSE
)

Arguments

spectral_count_object	List defined as "spectral_count_object" containing dataframes with abundance expressed as spectral counts organized by 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 variable name containing the conditions to be compared. This value corresponds to the name of one column from metadata.
list_conditions	Atomic vector indicating two conditions to A be compared. The first element is considered as the reference (denominator) for ratio calculations.
force	Logic value set at FALSE by default in order to ask permission to create object in the workstation of the user.

Value

A scatter plot (pdf) indicating the log2 (ratio + 1) of the entities (peptides, soubgroups, groups, taxonomic) between the two conditions provided.

Examples

data(fecal_waters)

plot_intensities_ratio(fecal_waters, "Methods", c("EF", "S"))

plot_intensities_ratio(fecal_waters, "SC_name", c("Q1", "Q2"))

metaprotr documentation built on Feb. 5, 2021, 9:06 a.m.