plotKS {benchdamic} | R Documentation

## plotKS

### Description

Draw the boxplots of the Kolmogorov-Smirnov test statistics for the p-value distributions across the mock comparisons.

### Usage

    plotKS(df_KS, cols = NULL)

### Arguments

`df_KS` | a `data.frame` produced by the `createTIEC` function containing the KS statistics and their p-values.
`cols` | named vector of colors.

### Value

A ggplot object.

### Examples

    # Load some data
    data(ps_stool_16S)

    # Generate the patterns for 10 mock comparison for an experiment
    # (N = 1000 is suggested)
    mocks <- createMocks(nsamples = phyloseq::nsamples(ps_stool_16S), N = 10)
    head(mocks)

    # Add some normalization/scaling factors to the phyloseq object
    my_norm <- setNormalizations(fun = c("norm_edgeR", "norm_CSS"),
        method = c("TMM", "median"))
    ps_stool_16S <- runNormalizations(normalization_list = my_norm,
        object = ps_stool_16S)

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

    # Run methods on mock datasets
    results <- runMocks(mocks = mocks, method_list = my_limma,
        object = ps_stool_16S)

    # Prepare results for Type I Error Control
    TIEC_summary <- createTIEC(results)

    # Plot the results
    plotFPR(df_FPR = TIEC_summary$df_FPR)
    plotQQ(df_QQ = TIEC_summary$df_QQ, zoom = c(0, 0.1))
    plotKS(df_KS = TIEC_summary$df_KS)

[Package benchdamic version 1.0.0 Index]