plot_venn: plot_venn

In metaprotr: Metaproteomics Post-Processing Analysis

Description

Generates a Venn diagram comparing up to 3 conditions. The lists of elements for each condition are also returned as a "venn_lists_object".

Usage

plot_venn(
  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 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 the explanatory variable that contains the conditions to be compared. This value corresponds to the name of one column from the metadata dataframe.
list_conditions	Atomic vector indicating the conditions to be compared. The provided elements (2 or 3) must be present in the variable indicated as "target_variable".
force	Logic value set at FALSE by default in order to ask permission to create a pdf file in the workstation of the user.

Value

A Venn diagram (pdf) and a list defined as "venn_list_object" containing the elements (peptides, soubgroups, groups or taxonomic levels) for each logical section of the Venn diagram (specific and intersections).

Examples

data(fecal_waters)
venn_QFW1_Q1 <- plot_venn(fecal_waters, "SC_name", c("Q1_FW1", "Q1"))

data(species_fw)
venn_all <- plot_venn(species_fw, "Methods", c("S_EF", "S", "EF"))

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