com_plot-mina: 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

## S4 method for signature 'mina,ANY'
com_plot(x, match, d1 = 1, d2 = 2, color, shape = NULL, ...)

## S4 method for signature 'mina,character'
com_plot(x, match, d1 = 1, d2 = 2, color, shape = NULL, ...)

## S4 method for signature 'mina,character'
com_plot(x, match, d1 = 1, d2 = 2, color, shape = NULL, ...)

Arguments

x	An object of 'mina' with list 'dmr' defined.
match	The column name of the components IDs in 'des' with exactly the same as rownames in x.
d1	The dimension be visualized in x-axis, default '1'.
d2	The dimension be visualized in y-axis, default '2'.
color	The column name in 'des' to be used for different color groups.
shape	The column name in 'des' to be used for different shape groups, default 'NULL'.
...	Additional parameters.

Value

p The plotted figure.

The PCoA plot.

Examples

maize <- new("mina", tab = maize_asv, des = maize_des)
maize <- norm_tab(maize, method = "raref")
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.