plotDists

Description

scatterplot showing distances between peaks

Usage

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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

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