plotDists {MMDiff2} | R Documentation |
scatterplot showing distances between peaks
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)
MD |
DBAmmd Object. This Object can be created using |
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) |
data("MMD") plotDists(MMD, whichContrast=1)