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
)

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