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)