plotDists {MMDiff2} | R Documentation

## plotDists

### Description

scatterplot showing distances between peaks

### Usage

    plotDists(MD, dist.method = "MMD", whichContrast = 1, which.group1 = NULL,
      which.group2 = NULL, diff.method = "MMD.locfit", bUsePval = FALSE,
      th = 0.1, title = NULL, what = 3, xlim = NULL, ylim = NULL,
      xlog10 = TRUE, Peak.IDs = NULL, withLegend = TRUE,
      shiny_df_opt = FALSE)

### Arguments

`MD` | DBAmmd Object. This Object can be created using `DBAmmd()`.
`dist.method` | specify method used for distances between samples. Currently only Maximum Mean Discrepancy (MMD) and Kolmogorov-Smirnov (KS) implemented. (DEFAULT: 'MMD')
`whichContrast` | index determining which of the set contrast should be used. (DEFAULT: 1)
`which.group1` | subset samples from group1 (DEFAULT: NULL)
`which.group2` | subset samples from group2 (DEFAULT: NULL)
`diff.method` | which method to use to determine significant peaks (DEFAULT: 'MMD.locfit')
`bUsePval` | if TRUE p-values instead of FDRs are used (DEFAULT: FALSE)
`th` | significance threshold for differential called peaks (DEFAULT: 0.1)
`title` | an overall title for the plot (DEFAULT: NULL)
`what` | which dists to overlay: 1: only between group distances, 2: between and within group distances, 3: between and within group distances, and significant peaks highlightend (DEFAULT: 3)
`xlim` | specify x range (DEFAULT: NULL)
`ylim` | specify y range (DEFAULT: NULL)
`xlog10` | should x range be plotted in log10 scale (DEFAULT: TRUE)
`Peak.IDs` | Highlight specific subset of peaks (DEFAULT: NULL)
`withLegend` | (DEFAULT: TRUE)
`shiny_df_opt` | Option returns a dataframe for shiny (DEFAULT: FALSE)

### Examples

    data("MMD")
    plotDists(MMD, whichContrast=1)

[Package MMDiff2 version 1.22.0 Index]