plotMotif: Correlation Motif plot

Description Usage Arguments Details Author(s) References Examples

View source: R/Cormotif.R

Description

This function plots the Correlation Motif patterns and the associated prior probability distributions.

Usage

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plotMotif(fitted_cormotif,title="")

Arguments

fitted_cormotif

The object obtained from cormotiffit.

title

The title for the graph.

Details

Each row in both graphs corresponds to one motif pattern. The left graph shows the correlation motif pattern. The grey color scale of cell (k,d) indicates the probability that motif k is differentially expressed in study d. Each row of the bar chart corresponds to the motif pattern in the same row of the left pattern graph. The length of the bar in the bar chart shows the number of genes of the given pattern in the dataset, which is equal to motif.fitted\$bestmotif\$motif.prior multiplying the number of total genes.

Author(s)

Hongkai Ji, Yingying Wei

References

Ji, H., Wei, Y.,(2011) Correlation Motif. Unpublished

Examples

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data(simudata2)
n<-nrow(simudata2)
m<-ncol(simudata2)
#the expression data is from the second column to m
exprs.simu2<-as.matrix(simudata2[,2:m])

#prepare the group ID number for each sample array
data(simu2_groupid)

#prepare the design matrix for each group of samples
data(simu2_compgroup)

#fit 2 correlation motif to the data
motif.fitted<-cormotiffit(exprs.simu2, simu2_groupid,simu2_compgroup,K=2)

plotMotif(motif.fitted)

Example output

Loading required package: affy
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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
[1] "We have run the first 50 iterations for K=2"

Cormotif documentation built on April 29, 2020, 5:20 a.m.