plot_pca: plot_pca

Description Usage Arguments Value Examples

View source: R/metaprotr_plot_pca.R

Description

Performs a Principal Components Analysis (PCA) from the spectral counts of the entities (peptides, subgroups, groups or taxonomic elements) in a "spectral_count_object" with or without taxonomy. PCA decomposition of high dimensional data allows to observe global effects in two dimensions. For more details of the used function check dudi.pca from ade4.

Usage

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plot_pca(spectral_count_object, colors_var, pc_components, force = FALSE)

Arguments

spectral_count_object

List described 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". The PCA projections will be applied to these observations.

colors_var

Character indicating the name of one column from metadata. The samples will be represented in different colors in function of the levels of this variable (ex. conditions).

pc_components

Two numeric values indicating two principal components to be analyzed.

force

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

Value

A pdf file containing the results of PCA applied to the two provided principal components. Including a bar plot indicating the percentage of variance per principal component.

Examples

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data(fecal_waters)
plot_pca(fecal_waters, "Methods", c(1, 2))

data(species_fw)
plot_pca(species_fw, "Methods", c(1, 3))

data(species_annot_fw)
plot_pca(species_annot_fw, "Condition", c(1, 2))

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