Description Usage Arguments Value Note Author(s) Examples
Plot analytes matrices
1 2 3 4 5 |
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$Meta to specify colors to be used |
deltaRT |
Censoring around the RT median |
linking |
Linking points from the specified sample type when injection order is on the x-axis |
orderBPlots |
Ordering barplots, default is sType foollowed by injection order |
cexBP |
cex.axis value for labelling x-axis of the BarPlots |
cexBX |
cex.axis value for labelling x-axis of the BoXplots |
cexEL |
cex for the Eic Legend |
cexPT |
cex for the PoinTs |
spacingBX |
relative spacing between points for the BoXplots |
... |
Arguments 1) used to match analytes and 2) passed to |
Experiment object
For graphing, any parameter that is equal to RT or starting by RT. will be considered as a retention time
David Enot david.enot@gustaveroussy.fr
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | testfiles=list.files(system.file( package = "GRMeta"),pattern = "txt$",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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.