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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(MMDiff2)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MMDiff2/plotDists.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDists
> ### Title: plotDists
> ### Aliases: plotDists
>
> ### ** Examples
>
> data("MMD")
> plotDists(MMD, whichContrast=1)
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.