This plot shows each gene as dot uniquely determined by its log2 fold change at the first level (represented on the x-axis) and the fold change at the second level (represented on the y-axis).
a character string specifying if the plot is saved in jpeg (jpeg), postscript (postscript), pdf (pdf) format, or it is simply displayed on the screen(on screen). By default this value is on screen.
track
a character vector of gene names that will be explicitly highlighted in the scatterplot, if they match any gene contained in the object of class DEGs. By default this vector is empty.
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)
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> library(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
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 object is masked from 'package:limma':
plotMA
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: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: org.Hs.eg.db
Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots
Attaching package: 'gplots'
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space
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Loading required package: plotrix
Attaching package: 'plotrix'
The following object is masked from 'package:gplots':
plotCI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/Scatterplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Scatterplot
> ### Title: ScatterplotHelpfile
> ### Aliases: Scatterplot
> ### Keywords: DEGs scatterplot fold change
>
> ### ** Examples
>
> data(tRanslatomeSampleData)
> Scatterplot(limma.DEGs, outputformat="on screen",track="")
Warning message:
In cor.test.default(vector1[list0], vector2[list0], method = "spearman") :
Cannot compute exact p-value with ties
>
>
>
>
>
> dev.off()
null device
1
>