plotConcordance {benchdamic} | R Documentation

## plotConcordance

### Description

Produce a list of graphical outputs summarizing the between and within method concordance.

### Usage

    plotConcordance(concordance, threshold = NULL, cols = NULL)

### Arguments

`concordance` | A long format `data.frame` produced by `createConcordance` function.
`threshold` | The threshold for rank (x-axis upper limit if all methods have a higher number of computed statistics).
`cols` | A named vector containing the color hex codes.

### Value

A 2 elements list of `ggplot2` class objects:

- `concordanceDendrogram` which contains the vertically directioned dendrogram for the methods involved in the concordance analysis;

- `concordanceHeatmap` which contains the heatmap of between and within method concordances.

### See Also

`createConcordance`

### Examples

    data(ps_plaque_16S)
    # Balanced design for independent samples
    my_splits <- createSplits(
        object = ps_plaque_16S, varName = "HMP_BODY_SUBSITE", balanced = TRUE,
        N = 10 # N = 100 suggested
    )

    # Initialize some limma based methods
    my_limma <- set_limma(design = ~ HMP_BODY_SUBSITE, coef = 2,
        norm = c("TMM", "CSSmedian"))

    # Set the normalization methods according to the DA methods
    my_norm <- setNormalizations(fun = c("norm_edgeR", "norm_CSS"),
        method = c("TMM", "median"))

    # Run methods on split datasets
    Plaque_16S_splitsDA <- runSplits(split_list = my_splits,
        method_list = my_limma, normalization_list = my_norm,
        object = ps_plaque_16S)

    # Concordance for p-values
    concordance_pvalues <- createConcordance(
        object = Plaque_16S_splitsDA, slot =
            "pValMat", colName = "rawP", type = "pvalue"
    )

    # plot concordances from rank 1 to 50.
    plotConcordance(
        concordance = concordance_pvalues,
        threshold = 50
    )

[Package benchdamic version 1.0.0 Index]