Create and plot diffusion maps

Description

The main function is DiffusionMap, which returns an object you can plot (plot.DiffusionMap is then called).

Details

The sigma parameter for DiffusionMap can be determined using find.sigmas if your dataset is small enough.

Examples

demo(destiny, ask = FALSE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(destiny)
Loading required package: Biobase
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

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/destiny/destiny.Rd_%03d_medium.png", width=480, height=480)
> ### Name: destiny
> ### Title: Create and plot diffusion maps
> ### Aliases: destiny destiny-package
> 
> ### ** Examples
> 
> demo(destiny, ask = FALSE)


	demo(destiny)
	---- ~~~~~~~

> library(destiny)

> library(RColorBrewer)

> data(guo)

> palette(brewer.pal(8L, 'Dark2'))

> sigmas <- find.sigmas(guo, censor.val = 15, censor.range = c(15, 40),
+                      verbose = FALSE)

> par(lwd = 3)

> plot(sigmas,
+ 		 col           = palette()[[1]],
+ 		 highlight.col = palette()[[4]],
+ 		 line.col      = palette()[[6]],
+      rect.options = list(border = 'white'))

> diff.guo <- DiffusionMap(guo, 11, censor.val = 15, censor.range = c(15, 40),
+                         verbose = FALSE)

> plot(diff.guo,
+      col = guo$num.cells, pch = 20)

> #library(rgl)
> #plot3d(eigenvectors(diff.guo)[, 1:3], col = guo$num.cells)
There were 15 warnings (use warnings() to see them)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>