pcoa_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.

Visulization of components distance / dissimilarity in k dimension.

Usage

pcoa_plot(x, des, match, ...)

## S4 method for signature 'list,data.frame,character'
pcoa_plot(x, des, match, d1 = 1, d2 = 2, color, shape = NULL, ...)

Arguments

x	A list generated by 'dmr'.
des	The corresponding descriptive table.
match	The column name of the components IDs in 'des' with exactly the same as rownames in x.
...	Additional parameters.
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'.

Value

p The plotted figure.

p The plotted PCoA.

Examples

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

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