Re: [R] Problem with colors in contour plot
On 10/04/2012 10:25 PM, Loukia Spineli wrote: Dear R users, I have a 51 by 51 matrix of p-values (named as pvalue_MA). I want to present graphically this matrix in a plot (filled contour plot) where both axes represent probabilities. I have also added a grid in this plot. I want to highlight in white the cells of the grid that represent p-values smaller than the (common) significance threshold, 0.05. The code from this plot is colored in blue (I had to copy-pasted all this code in order to reach to the plot). I suspect that the problem might be in the col parameter of the filled.contour function. Honestly, I cannot understand why the plot appears to be completely white!! I checked the values of my variable and it has a great range from 0 to 1. Any suggestion/ comment would really help me to move on with my project. Hi Loukia, Do you really need a contour plot for this? pvals-matrix(runif(2601),nrow=51) library(plotrix) pcols-ifelse(pvals=0.05,white,gray) color2D.matplot(pvals,cellcolors=pcols) Jim __ 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] Problem with colors in contour plot
Thank you very much Jim!!! Your function achieves to color the grid tha way I want, but it can handle only one variable, if I have understood correctly the details of this function.The plot must display in the axes percentages and in the grids pvalues. I have incorporated 3 different variables in a contourplot. On Fri, Oct 5, 2012 at 12:08 PM, Jim Lemon j...@bitwrit.com.au wrote: On 10/04/2012 10:25 PM, Loukia Spineli wrote: Dear R users, I have a 51 by 51 matrix of p-values (named as pvalue_MA). I want to present graphically this matrix in a plot (filled contour plot) where both axes represent probabilities. I have also added a grid in this plot. I want to highlight in white the cells of the grid that represent p-values smaller than the (common) significance threshold, 0.05. The code from this plot is colored in blue (I had to copy-pasted all this code in order to reach to the plot). I suspect that the problem might be in the col parameter of the filled.contour function. Honestly, I cannot understand why the plot appears to be completely white!! I checked the values of my variable and it has a great range from 0 to 1. Any suggestion/ comment would really help me to move on with my project. Hi Loukia, Do you really need a contour plot for this? pvals-matrix(runif(2601),**nrow=51) library(plotrix) pcols-ifelse(pvals=0.05,**white,gray) color2D.matplot(pvals,**cellcolors=pcols) Jim [[alternative HTML version deleted]] __ 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] Problem with colors in contour plot
Dear R users, I have a 51 by 51 matrix of p-values (named as pvalue_MA). I want to present graphically this matrix in a plot (filled contour plot) where both axes represent probabilities. I have also added a grid in this plot. I want to highlight in white the cells of the grid that represent p-values smaller than the (common) significance threshold, 0.05. The code from this plot is colored in blue (I had to copy-pasted all this code in order to reach to the plot). I suspect that the problem might be in the col parameter of the filled.contour function. Honestly, I cannot understand why the plot appears to be completely white!! I checked the values of my variable and it has a great range from 0 to 1. Any suggestion/ comment would really help me to move on with my project. All the best, Loukia __ 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] Problem with colors in contour plot
Hello,
Something like this?
myRamp - colorRampPalette(c(lightblue, darkblue))
mypal - myRamp(20)
mypal[1] - rgb(1, 1, 1)
#?filled.contour
## Persian Rug Art:
x - y - seq(-4*pi, 4*pi, len = 27)
r - sqrt(outer(x^2, y^2, +))
filled.contour(cos(r^2)^2, frame.plot = FALSE,
plot.axes = {}, col = mypal)
grid()
Hope this helps,
Rui Barradas
Em 04-10-2012 13:25, Loukia Spineli escreveu:
Dear R users,
I have a 51 by 51 matrix of p-values (named as pvalue_MA). I want to
present graphically this matrix in a plot (filled contour plot) where both
axes represent probabilities. I have also added a grid in this plot. I want
to highlight in white the cells of the grid that represent p-values smaller
than the (common) significance threshold, 0.05. The code from this plot is
colored in blue (I had to copy-pasted all this code in order to reach to
the plot). I suspect that the problem might be in the col parameter of
the filled.contour function. Honestly, I cannot understand why the plot
appears to be completely white!! I checked the values of my variable and it
has a great range from 0 to 1.
Any suggestion/ comment would really help me to move on with my project.
All the best,
Loukia
__
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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.
[[alternative HTML version deleted]]
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Re: [R] Problem with colors in contour plot
The contpour plot is very impressive!!! The contour plot I want to display
should have only 2 colors: white a grey. I have created this plot for only
one trial (see, ppts) and now I am attempting to do the same for many
trials.
On Thu, Oct 4, 2012 at 3:51 PM, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
Something like this?
myRamp - colorRampPalette(c(lightblue, darkblue))
mypal - myRamp(20)
mypal[1] - rgb(1, 1, 1)
#?filled.contour
## Persian Rug Art:
x - y - seq(-4*pi, 4*pi, len = 27)
r - sqrt(outer(x^2, y^2, +))
filled.contour(cos(r^2)^2, frame.plot = FALSE,
plot.axes = {}, col = mypal)
grid()
Hope this helps,
Rui Barradas
Em 04-10-2012 13:25, Loukia Spineli escreveu:
Dear R users,
I have a 51 by 51 matrix of p-values (named as pvalue_MA). I want to
present graphically this matrix in a plot (filled contour plot) where both
axes represent probabilities. I have also added a grid in this plot. I want
to highlight in white the cells of the grid that represent p-values smaller
than the (common) significance threshold, 0.05. The code from this plot is
colored in blue (I had to copy-pasted all this code in order to reach to
the plot). I suspect that the problem might be in the col parameter of
the filled.contour function. Honestly, I cannot understand why the plot
appears to be completely white!! I checked the values of my variable and it
has a great range from 0 to 1.
Any suggestion/ comment would really help me to move on with my project.
All the best,
Loukia
__r-h...@r-project.org mailing
listhttps://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.
Re: [R] problem with colors
Hi Phil and Thomas, Thanks for your helpful feedback. I must admit my solution to creating the vector of colors lacked your elegance. In brief, I saved the output of colors() into a text file, saved all but 47 colours in that file and read it back as a data frame and used the first column of the dataframe as a vector of 47 colours. This roundabout method may have caused the problem because when I chose colours according to the commands sent by both of you things seemed to work just fine. Thank you very much for your feedback. Anjan On Thu, Oct 7, 2010 at 3:25 PM, Thomas Stewart tgstew...@gmail.com wrote: I would be helpful if you provided a more complete, reproducible example. Consider the following code. It colors the boxes according to the first 47 colors listed in the color() vector. -tgs data-as.data.frame(matrix(rnorm(47*23),ncol=47)) boxplot(data,col=colors()[1:47]) On Thu, Oct 7, 2010 at 2:22 PM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, I have a data set of 47 columns. I would like to create a boxplot for each column, each boxplot of a different colour. So I created a vector col1. This vector has a subset of the colors returned by color()- red, cyan, green etc. Now I use the command: boxplot(dataset, col= col1) expecting to see 47 boxplots, each of a different colour. Here is the problem: the boxplots are drawn correctly but it seems that only the first few colours in col1 are being used in a repeated pattern. Anybody has any ideas on how to tackle this? Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ 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. -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ 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] problem with colors
Hi, I have a data set of 47 columns. I would like to create a boxplot for each column, each boxplot of a different colour. So I created a vector col1. This vector has a subset of the colors returned by color()- red, cyan, green etc. Now I use the command: boxplot(dataset, col= col1) expecting to see 47 boxplots, each of a different colour. Here is the problem: the boxplots are drawn correctly but it seems that only the first few colours in col1 are being used in a repeated pattern. Anybody has any ideas on how to tackle this? Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ 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] problem with colors
Anjan - I think you'll need to give us more information -- I can't reproduce the problem. For example, dat = data.frame(matrix(rnorm(47000),100,47)) cols = sample(colors(),47) boxplot(dat,col=cols) doesn't repeat any of the colors in cols. - Phil On Thu, 7 Oct 2010, ANJAN PURKAYASTHA wrote: Hi, I have a data set of 47 columns. I would like to create a boxplot for each column, each boxplot of a different colour. So I created a vector col1. This vector has a subset of the colors returned by color()- red, cyan, green etc. Now I use the command: boxplot(dataset, col= col1) expecting to see 47 boxplots, each of a different colour. Here is the problem: the boxplots are drawn correctly but it seems that only the first few colours in col1 are being used in a repeated pattern. Anybody has any ideas on how to tackle this? Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ 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.
Re: [R] problem with colors
I would be helpful if you provided a more complete, reproducible example. Consider the following code. It colors the boxes according to the first 47 colors listed in the color() vector. -tgs data-as.data.frame(matrix(rnorm(47*23),ncol=47)) boxplot(data,col=colors()[1:47]) On Thu, Oct 7, 2010 at 2:22 PM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, I have a data set of 47 columns. I would like to create a boxplot for each column, each boxplot of a different colour. So I created a vector col1. This vector has a subset of the colors returned by color()- red, cyan, green etc. Now I use the command: boxplot(dataset, col= col1) expecting to see 47 boxplots, each of a different colour. Here is the problem: the boxplots are drawn correctly but it seems that only the first few colours in col1 are being used in a repeated pattern. Anybody has any ideas on how to tackle this? Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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.
