pcoa_plot {mina} | R Documentation

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

### 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")

[Package mina version 1.2.0 Index]