[R] automatically adjusting axis limits
Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 5 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (5 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and Reflectance (56x5). I would like to plot Reflectance vs Wavelength i.e. overlay 5 spectra one one top of the other. plot(Wavelength, Reflectance) does not work (Matlab would do it): Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ I then tried to construct the two matrices so that they have the same size (56x5) and plot it all at once with the command plot. This works but it is such a computationally inefficient way that I do not want to do this Why redundantly store wavelength data? Later I will have to process much more spectra so this is not a good practice for me. I then decided to draw the first spectra on the first run of the for loop with the command plot and add the subsequent graphs with the command lines. This works but the y-axes limits do not adjust automatically, leaving many spectra out of the axis limits ;( I don't want to set the axis limits by hand as I need this script to be completely autonomous. I don't want to program lines of code to calculate those limits myself either I am sure the mighty R can do it... BUT HOW (Matlab would easily do it with a single command) What I need is a command that will redraw the graph by automatically adjusting the axis limits. I have been searching for many days on the web, forums and mailing list archives but I still don't know how to do it. Please help thanks a lot from advance for your kindly help Servet __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] automatically adjusting axis limits
Sac-6 wrote: Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 5 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (5 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and Reflectance (56x5). I would like to plot Reflectance vs Wavelength i.e. overlay 5 spectra one one top of the other. plot(Wavelength, Reflectance) does not work (Matlab would do it): Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ I then tried to construct the two matrices so that they have the same size (56x5) and plot it all at once with the command plot. This works but it is such a computationally inefficient way that I do not want to do this Why redundantly store wavelength data? Later I will have to process much more spectra so this is not a good practice for me. I then decided to draw the first spectra on the first run of the for loop with the command plot and add the subsequent graphs with the command lines. This works but the y-axes limits do not adjust automatically, leaving many spectra out of the axis limits ;( I don't want to set the axis limits by hand as I need this script to be completely autonomous. I don't want to program lines of code to calculate those limits myself either I am sure the mighty R can do it... BUT HOW (Matlab would easily do it with a single command) What I need is a command that will redraw the graph by automatically adjusting the axis limits. I have been searching for many days on the web, forums and mailing list archives but I still don't know how to do it. Please help thanks a lot from advance for your kindly help Servet Are all the wavelengths the same? The best answer is matplot(), but you need to reformat your data a bit. for example: files - list.files(pattern=[something appropriate]) datlist - lapply(files,read.table,...[other arguments such as header=TRUE]) wavelens - datlist[[1]][,1] datlist2 - lapply(datlist,[[,vals]] ## assuming second column is called vals datmat - do.call(datlist2,cbind) matplot(wavelens,datmat) -- View this message in context: http://www.nabble.com/automatically-adjusting-axis-limits-tp26082508p26083141.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] automatically adjusting axis limits
Sac-6 wrote: Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 5 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (5 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and Reflectance (56x5). I would like to plot Reflectance vs Wavelength i.e. overlay 5 spectra one one top of the other. plot(Wavelength, Reflectance) does not work (Matlab would do it): Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ I then tried to construct the two matrices so that they have the same size (56x5) and plot it all at once with the command plot. This works but it is such a computationally inefficient way that I do not want to do this Why redundantly store wavelength data? Later I will have to process much more spectra so this is not a good practice for me. I then decided to draw the first spectra on the first run of the for loop with the command plot and add the subsequent graphs with the command lines. This works but the y-axes limits do not adjust automatically, leaving many spectra out of the axis limits ;( I don't want to set the axis limits by hand as I need this script to be completely autonomous. I don't want to program lines of code to calculate those limits myself either I am sure the mighty R can do it... BUT HOW (Matlab would easily do it with a single command) What I need is a command that will redraw the graph by automatically adjusting the axis limits. I have been searching for many days on the web, forums and mailing list archives but I still don't know how to do it. Please help thanks a lot from advance for your kindly help Servet oops, I wasn't reading carefully enough, you've already done all the hard work. matplot(Wavelength,Reflectance) -- View this message in context: http://www.nabble.com/automatically-adjusting-axis-limits-tp26082508p26083157.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] automatically adjusting axis limits
PLEASE provide commented, minimal, self-contained, reproducible code. particularly a sample data.set. At the moment it sounds like you have one variable (Wavelength) with a length of 56 and Reflectance with a length of 5,000. What format(s) are the data in? Data.frames? Clearly this is not the case but I don't understand the data layout at all --- On Tue, 10/27/09, Servet Ahmet Cizmeli sa.cizm...@usherbrooke.ca wrote: From: Servet Ahmet Cizmeli sa.cizm...@usherbrooke.ca Subject: [R] automatically adjusting axis limits To: r-help@r-project.org Received: Tuesday, October 27, 2009, 2:12 PM Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 5 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (5 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and Reflectance (56x5). I would like to plot Reflectance vs Wavelength i.e. overlay 5 spectra one one top of the other. plot(Wavelength, Reflectance) does not work (Matlab would do it): Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ I then tried to construct the two matrices so that they have the same size (56x5) and plot it all at once with the command plot. This works but it is such a computationally inefficient way that I do not want to do this Why redundantly store wavelength data? Later I will have to process much more spectra so this is not a good practice for me. I then decided to draw the first spectra on the first run of the for loop with the command plot and add the subsequent graphs with the command lines. This works but the y-axes limits do not adjust automatically, leaving many spectra out of the axis limits ;( I don't want to set the axis limits by hand as I need this script to be completely autonomous. I don't want to program lines of code to calculate those limits myself either I am sure the mighty R can do it... BUT HOW (Matlab would easily do it with a single command) What I need is a command that will redraw the graph by automatically adjusting the axis limits. I have been searching for many days on the web, forums and mailing list archives but I still don't know how to do it. Please help thanks a lot from advance for your kindly help Servet __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ Looking for the perfect gift? Give the gift of Flickr! http://www.flickr.com/gift/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] automatically adjusting axis limits
If you really want to update the range of the plot axes after plotting, there is the zoomplot function in the TeachingDemos package. You will need to update the y-range each time through the loop and pass that to zoomplot. But, matplot is the better overall solution as has been pointed out already. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Servet Ahmet Cizmeli Sent: Tuesday, October 27, 2009 12:13 PM To: r-help@r-project.org Subject: [R] automatically adjusting axis limits Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 5 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (5 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and Reflectance (56x5). I would like to plot Reflectance vs Wavelength i.e. overlay 5 spectra one one top of the other. plot(Wavelength, Reflectance) does not work (Matlab would do it): Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ I then tried to construct the two matrices so that they have the same size (56x5) and plot it all at once with the command plot. This works but it is such a computationally inefficient way that I do not want to do this Why redundantly store wavelength data? Later I will have to process much more spectra so this is not a good practice for me. I then decided to draw the first spectra on the first run of the for loop with the command plot and add the subsequent graphs with the command lines. This works but the y-axes limits do not adjust automatically, leaving many spectra out of the axis limits ;( I don't want to set the axis limits by hand as I need this script to be completely autonomous. I don't want to program lines of code to calculate those limits myself either I am sure the mighty R can do it... BUT HOW (Matlab would easily do it with a single command) What I need is a command that will redraw the graph by automatically adjusting the axis limits. I have been searching for many days on the web, forums and mailing list archives but I still don't know how to do it. Please help thanks a lot from advance for your kindly help Servet __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
