plot.tsp: Graphical display of tsp objects

In tspair: Top Scoring Pairs for Microarray Classification

Description

Graphical display of tsp objects

Usage

  ## S3 method for class 'tsp'
plot(x,y,...)

Arguments

x	A tsp object
y	Not used
...	Plotting arguments, not used

Details

tspplot() creates a plot of each top scoring pair.The figure plots the expression for the first gene in the TSP pair versus the expression for the second gene in the TSP pair across arrays. The user defined groups are plotted in the colors red and blue. The score for the pair is shown across the top of each plot. If there is more than one TSP, hitting return will cycle from one TSP to the next.

Value

Nothing of interest.

Author(s)

Jeffrey T. Leek [e-mail]

References

D. Geman, C. d'Avignon, D. Naiman and R. Winslow, "Classifying gene expression profiles from pairwise mRNA comparisons, Statist. Appl. in Genetics and Molecular Biology, 3, 2004.

See Also

tspcalc, ts.pair, tspsig,predict.tsp, summary.tsp, tspplot

Examples

  ## Not run: 
  ## Load data
  data(tspdata) 
  tsp1 <- tspcalc(dat,grp)
  plot(tsp1)
 
## End(Not run)

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning message:
In if (class(dat) == "ExpressionSet") { :
  the condition has length > 1 and only the first element will be used
Number of TSPs:  1 
TSP 1 

tspair documentation built on Nov. 8, 2020, 6:51 p.m.