massi_cluster_plot

Description

This function produces three figures in a new graphics device to enable the exploration of the massi_cluster and massi_select results.

Usage

massi_cluster_plot(massi_select_data, massi_cluster_data)

Arguments

Details

The first figure is a heatmap depicting probe values for each sample. The second figure is a bar plot showing the mean probe expression and standard deviation for each sample. The bars are colored with respect to the predicted sex. The third figure is a principal component plot which represents the distances bewteen samples, with each cluster highlighted with elipses.

Value

Returns three plots in a new graphics device.

Author(s)

Sam Buckberry

References

Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2013). gplots: Various R programming tools for plotting data. R package version 2.12.1. http://CRAN.R-project.org/package=gplots

See Also

massi_cluster, massi_select

Examples

# load the test dataset
data(massi.test.dataset, massi.test.probes)

# select the y chromosome probes using massi_select
massi_select_out <- 
massi_select(massi.test.dataset, massi.test.probes)

# cluster samples to predict sex using massi_cluster
massi_cluster_out <- 
massi_cluster(massi_select_out)

# produce plots using massi_cluster_plot
massi_cluster_plot(massi_select_out, massi_cluster_out)

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(massiR)
Loading required package: cluster
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: diptest
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/massiR/massi_cluster_plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: massi_cluster_plot
> ### Title: massi_cluster_plot
> ### Aliases: massi_cluster_plot
> 
> ### ** Examples
> 
> 
> # load the test dataset
> data(massi.test.dataset, massi.test.probes)
> 
> # select the y chromosome probes using massi_select
> massi_select_out <- 
+ massi_select(massi.test.dataset, massi.test.probes)
> 
> # cluster samples to predict sex using massi_cluster
> massi_cluster_out <- 
+ massi_cluster(massi_select_out)
> 
> # produce plots using massi_cluster_plot
> massi_cluster_plot(massi_select_out, massi_cluster_out)
Error in dev.new() : no suitable unused file name for pdf()
Calls: massi_cluster_plot -> dev.new
Execution halted