plot.metaboSet: Plot analyte data from a metaboSet object

In tonedivad/GRMeta: Processing MetX data

Description

Plot analytes matrices

Usage

## S3 method for class 'metaboSet'
plot(obj,outfile=NULL,
                         lgraphs=list(c("RT~InjOrder"),c("Area~InjOrder",log="y"),c("Area~1",log="y"),c("Height~Area",log="xy")),
                         mfrow=c(2,2),colorCol=NULL,deltaRT=0.05,linking="QC",orderBPlots=c("sType","InjOrder"),
                         cexBP=0.5,cexBX=.8,cexEL=0.4,cexPT=1.5,...)

Arguments

obj	Experiment obj
outfile	PDF file: if not given results are graphed in the environment
lgraphs	List of size vectors for plotting in form of y~x. Optionally 2 second argments is for controlling the log scale
mfrow	Distribution of the plots on the figure
colorCol	Column in obj$Meta to specify colors to be used
deltaRT	Censoring around the RT median
linking	Linking points from the specified sample type when injection order is on the x-axis
orderBPlots	Ordering barplots, default is sType foollowed by injection order
cexBP	cex.axis value for labelling x-axis of the BarPlots
cexBX	cex.axis value for labelling x-axis of the BoXplots
cexEL	cex for the Eic Legend
cexPT	cex for the PoinTs
spacingBX	relative spacing between points for the BoXplots
...	Arguments 1) used to match analytes and 2) passed to par and pdf, excepted mfrow

Value

Experiment object

Note

For graphing, any parameter that is equal to RT or starting by RT. will be considered as a retention time

Author(s)

David Enot [e-mail]

Examples

testfiles=list.files(system.file( package = "GRMeta"),pattern = "txt$",full.names = TRUE)
mydata=loadAgilentData(ifile =testfiles[1])
mydata$Analyte

analyte=mydata$Analyte[2]
## Not run: 
plot(mydata,Analyte=mydata$Analyte[2],
    lgraphs=list(c("RT~InjOrder"),c("Area~InjOrder",log="y"),c("Height"),c("Height~Area",log="xy")),
                         mfrow=c(2,2),deltaRT=0.05,linking="QC")
                         

## End(Not run)
## Not run: 
#### sType: character
#### sTypeFac: factor
mydata$Meta$sTypeFac=factor(mydata$Meta$sType)
plot(mydata,Analyte=mydata$Analyte[2],
    lgraphs=list(c("Area",log="y"),c("Area~Sid",log="y"),
      c("Area~sType",log="y"),c("Area~sTypeFac",log="y")),
      mfrow=c(2,2),orderBPlots=c("sType","InjOrder"))
      
#### Only 1 boxplot -> mfrow=c(1,1)
plot(mydata,Analyte=mydata$Analyte[2],
    lgraphs=list(c("Area~sTypeFac",log="y")),
      mfrow=c(1,1))

## End(Not run)
#### Dump them all in a file:  by default all of them
## Not run: 
plot(mydata,outfile="DumpAll.pdf",cex.main=1,height=8,cexBP = 0.4)

## End(Not run)

tonedivad/GRMeta documentation built on May 31, 2019, 6:21 p.m.