R: Scatterplot of SpC means comparing two conditions
spc.scatterplot
R Documentation
Scatterplot of SpC means comparing two conditions
Description
Given a SpC matrix and a two levels factor, draws a scatterplot with SpC means
of one condition in the x axis and SpC means of the second condition in the y
axis.
A SpC matrix with proteins in the rows and samples in the columns.
treat
A two level factor of length equal to the number of columns in the expression
matrix. The two levels represent the conditions to be compared.
trans
The transformation made on the means before plotting. One among "log2", "sqrt",
or "none". The default is "log2".
minSpC
Used as signal threshold.
minLFC
Used as size effect threshold.
...
Extra parameters passed to the plot function.
Details
The transformed means are plotted, one condition versus the other. The borders
representing absolute log fold change 1 are drawn as dashed lines.
All features with log fold change equal to or greather than minLFC and with
mean SpC in the most abundant condition equal to or greather than minSpC
are colored in red.
Author(s)
Josep Gregori
Examples
data(msms.dataset)
spc.scatterplot(exprs(msms.dataset),treat=pData(msms.dataset)[,1],trans="log2",
minSpC=2,minLFC=1,main="UPS1 200fm vs 600fm")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(msmsEDA)
Loading required package: MSnbase
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
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: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/msmsEDA/spc.scatterplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spc.scatterplot
> ### Title: Scatterplot of SpC means comparing two conditions
> ### Aliases: spc.scatterplot
> ### Keywords: plots
>
> ### ** Examples
>
> data(msms.dataset)
> spc.scatterplot(exprs(msms.dataset),treat=pData(msms.dataset)[,1],trans="log2",
+ minSpC=2,minLFC=1,main="UPS1 200fm vs 600fm")
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.