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Barplot Labels Problem
6 messages · Rodrigo Aluizio, Fernando Marmolejo Ramos, Ben Bolker +2 more
Dear R team Jim Lemon recently said regarding new improvements in PrettyR and plotrix: ?Remember, it is your whingeing and moaning that have helped to make these packages what they are today.? So, this is my whinge: out there is a freeware called Vista, which runs, among other things, bootstrap analyses. Most of the numerical reports given by Vista can be done using packages such as ?boot?, ?bootstrap?, and ?simpleboot?. I?ve not explored all the functions in these packages thoroughly (very casually), but the first thing I noticed is that the graphical output is majorly histograms. Vista offers a so-called Multiple Visualisation (MV) of the output of a bootstrap (it shows on the same window scatter plots for a particular variable showing the bootstrapped CI, a scatter plot of the evolution of the bootstrapped mean over many sample sizes, a box plot, a QQ plot, and a histogram). I wonder if there is any manner in which this sort of MV could me mimicked by R in the case of bootstrap. My best guess is that I?d have to create a 3 by 2 frame an insert each graph separately or maybe resort to Trellis graphics am I right? Does anyone have a more sophisticated solution? Cheers, Fer
Fernando Marmolejo Ramos <fernando.marmolejoramos <at> adelaide.edu.au> writes:
Dear R team
Vista offers a so-called Multiple Visualisation (MV) of the output of a bootstrap (it shows on the same window scatter plots for a particular variable showing the bootstrapped CI, a scatter plot of the evolution of the bootstrapped mean over many sample sizes, a box plot, a QQ plot, and a histogram). I wonder if there is any manner in which this sort of MV could me mimicked by R in the case of bootstrap. My best guess is that I?d have to create a 3 by 2 frame an insert each graph separately or maybe resort to Trellis graphics
am I
right? Does anyone have a more sophisticated solution?
I'm not sure this is the right kind of problem for Trellis graphics (which are geared toward using the same plot type for different subsets of the data in each panel, rather than different plot types of the same data). The "unsophisticated" solution (which seems just fine), as you suggest, is to use par(mfrow) or par(mfcol) to break up the plot window into frames, and then plot the different bits in each window. See http://emdbolker.wikidot.com/blog:dynamite for an example of plotting the same data in different ways within subplots (and http://emdbolker.wdfiles.com/local--files/blog:dynamite/barboxdotviolin.R for the code). As far as R is concerned, "sophisticated" would mean creating a plotting function for this so that you never had to look at the details again ... Ben Bolker
Or if you want the plots to not all be the same size and line up in various ways (boxplots as margins of scatter plot, etc.) then look at the layout function. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.snow at imail.org 801.408.8111
-----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- project.org] On Behalf Of Ben Bolker Sent: Friday, October 24, 2008 8:14 AM To: r-help at stat.math.ethz.ch Subject: Re: [R] multiple visualisation of a bootstrap Fernando Marmolejo Ramos <fernando.marmolejoramos <at> adelaide.edu.au> writes:
Dear R team
Vista offers a so-called Multiple Visualisation (MV) of the output of
a
bootstrap (it shows on the same window scatter plots for a particular
variable
showing the bootstrapped CI, a scatter plot of the evolution of the bootstrapped mean over many sample sizes, a box plot, a QQ plot, and a histogram). I wonder if there is any manner in which this sort of MV could me mimicked by R in the case of bootstrap. My best guess is that I?d have to create a
3 by 2
frame an insert each graph separately or maybe resort to Trellis graphics
am I
right? Does anyone have a more sophisticated solution?
I'm not sure this is the right kind of problem for Trellis graphics (which are geared toward using the same plot type for different subsets of the data in each panel, rather than different plot types of the same data). The "unsophisticated" solution (which seems just fine), as you suggest, is to use par(mfrow) or par(mfcol) to break up the plot window into frames, and then plot the different bits in each window. See http://emdbolker.wikidot.com/blog:dynamite for an example of plotting the same data in different ways within subplots (and http://emdbolker.wdfiles.com/local-- files/blog:dynamite/barboxdotviolin.R for the code). As far as R is concerned, "sophisticated" would mean creating a plotting function for this so that you never had to look at the details again ... Ben Bolker
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Rodrigo Aluizio wrote:
Hi everybody, well I'm trying to use barplot for the first time. I get a suitable graphic but I'm having a weird problem. My graphic is generated from a matrix with several species (rowNames) and two abundance columns. So each species will have two bars, and the species name should appear at left. Until now everything is Ok, but when a I plot it the species names (my labels) are cut by device limits, and only part of the names appear. I could move them with the command "line=some negative value", but the axis (x and y) stay put and the things get over each other (the command 'line' works, but a error saying that it's not a graphic parameter appears). In addition, but with less importance, how could I remove the legend borders? And why, when I try use the 'width' command it fails to raise the width of the bars and I get and error saying that its not a graphic parameter (the command is in barplot help!!)? I'm using R 2.8.0 at Windows XP 32 bits. Here is the code I'm using, where MainSpp is my matrix: barplot(MainSpp,horiz=T,beside=T,main='Main Species',xlab='%',las=1, legend.text=T,width=5,cex.names=0.8)
Hi Rodrigo, I think that the staxlab function in the plotrix package might do what you want. For the legend problem, I would suggest not using the barplot legend option but using the legend function with bty="n". Jim
1 day later
Thanks for the help Jim, The legend function solved the legend border problem but the labels, even using staxlab from plotrix are still being cut by the device limits, like there is some kind of character number limits or something like that. Anyway thank you so much, I'll keep trying and searching. Rodrigo. -------------------------------------------------- From: "Jim Lemon" <jim em bitwrit.com.au> Sent: Saturday, October 25, 2008 9:16 AM To: "Rodrigo Aluizio" <r.aluizio em gmail.com> Cc: "R Help" <r-help em r-project.org> Subject: Re: [R] Barplot Labels Problem
Rodrigo Aluizio wrote:
Hi everybody, well I'm trying to use barplot for the first time. I get a suitable graphic but I'm having a weird problem. My graphic is generated from a matrix with several species (rowNames) and two abundance columns. So each species will have two bars, and the species name should appear at left. Until now everything is Ok, but when a I plot it the species names (my labels) are cut by device limits, and only part of the names appear. I could move them with the command "line=some negative value", but the axis (x and y) stay put and the things get over each other (the command 'line' works, but a error saying that it's not a graphic parameter appears). In addition, but with less importance, how could I remove the legend borders? And why, when I try use the 'width' command it fails to raise the width of the bars and I get and error saying that its not a graphic parameter (the command is in barplot help!!)? I'm using R 2.8.0 at Windows XP 32 bits. Here is the code I'm using, where MainSpp is my matrix: barplot(MainSpp,horiz=T,beside=T,main='Main Species',xlab='%',las=1, legend.text=T,width=5,cex.names=0.8)
Hi Rodrigo, I think that the function in the plotrix package might do what you want. For the legend problem, I would suggest not using the barplot legend option but using the legend function with bty="n". Jim