com_plot: Visulization of components distance / dissimilarity in k...

In Guan06/mina: Microbial community dIversity and Network Analysis

Description

Visulization of components distance / dissimilarity in k dimension.

Usage

com_plot(x, match, ...)

Arguments

x	An object of class 'mina' with 'dmr' and 'des' defined.
match	The column name of the components IDs in 'des' which exactly the same indicated in 'dmr'.
...	Additional parameters.

Value

The PCoA plot.

Examples

maize <- new("mina", tab = maize_asv2, des = maize_des2)
maize <- norm_tab(maize, method = "raref", depth = 5000)
maize <- fit_tabs(maize)
maize <- com_dis(maize, method = "bray")
maize <- dmr(maize)
p1a <- com_plot(maize, match = "Sample_ID", color = "Compartment")
p1b <- com_plot(maize, match = "Sample_ID", d1 = 3, d2 = 4,
color = "Compartment")
p2a <- com_plot(maize, match = "Sample_ID", color = "Host_genotype")
p2b <- com_plot(maize, match = "Sample_ID", d1 = 1, d2 = 3, color =
"Host_genotype")
p3a <- com_plot(maize, match = "Sample_ID", color = "Compartment", shape =
"Soil")
p3b <- com_plot(maize, match = "Sample_ID", d1 = 1, d2 = 4, color =
"Compartment", shape = "Soil")

Guan06/mina documentation built on Feb. 21, 2022, 11:56 a.m.