Print Page - centwave peakpicking figures

Title: centwave peakpicking figures
Post by: benlh on January 08, 2013, 02:30:12 AM

I just have a trivial question : how do you generate images like in this post http://http://metabolomics-forum.com/viewtopic.php?f=25&t=222&sid=5542c1121e2bee6204c7f0712695366c ?
I would like to be able able to do such files in order to control my peak picking parameters.

thanks a lot for your help.

Title: Re: centwave peakpicking figures
Post by: Ralf on January 08, 2013, 04:53:52 PM

Set the sleep parameter to a value greater zero, e.g. sleep=1.

Title: Re: centwave peakpicking figures
Post by: benlh on January 10, 2013, 10:21:11 AM

thanks for the information. It works very well.
but could it be possible to perform such figures manually on selected chromatographic peks ?

Title: Re: centwave peakpicking figures
Post by: Ralf on January 10, 2013, 01:24:03 PM

not really. but you can use something like

Code: [Select]

jpeg(file="EIC%d.jpeg")
xcmsSet(..., sleep=0.01)
dev.off()

to have the plots for each feature saved to jpeg files (EIC1.jpeg, EIC2.jpeg, ... etc.).

Title: Re: centwave peakpicking figures
Post by: sneumann on January 10, 2013, 02:12:48 PM

... and with scanrange=c(x,y) you can limit to the region of a particular peak.

Yours,
Steffen

Title: Re: centwave peakpicking figures
Post by: benlh on January 11, 2013, 02:31:03 AM

many thanks for your help

Metabolomics Society Forum

Software => R => XCMS => Topic started by: benlh on January 08, 2013, 02:30:12 AM