com_plot,mina,ANY-method {mina} | R Documentation

## Visulization of components distance / dissimilarity in k dimension.

### 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")

[Package mina version 1.2.0 Index]