Re: [R] ggplot2 customizing a plot
Hello Ista, I would like to thank you for your reply! Your code is indeed an improvement. This is my code now and there are two things still missing. DataToPlot-matrix(data=runif(9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) cols-colours() cols-cols[1:(nrow(DataToPlot)*ncol(DataToPlot))] tdm-melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=cols,breaks=c(1,0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1,0)) My values go from 0 to 1 (might go slightly over the limits) and I want to specify one color for the following ranges, 1, 0.9,0.8,.,0 . That means that values between the intervals will be categorized based on their closest match. What I also tried is to create a gray scale pallete as this is printer friendly so the values from 0.9 to 0.1 get a greyish tone but I failed to do that with colours. Could you please help me have both a. A fixed scale where values are categorized there and b. a greyish pallete for the categories? I would like to thank you in advance for your reply Regards Alex From: Ista Zahn istaz...@gmail.com Cc: R help R-help@r-project.org Sent: Wednesday, February 20, 2013 4:54 PM Subject: Re: [R] ggplot2 customizing a plot Hi, Dear all, I want some help improve my ggplot as following: Make the plottable area with grid, so is easy one to see where each box refers to x and y values. I don't think you can easily move the grid to the front, but you can make the tiles transparent so the grid can be seen through them by setting the alpha 1. Add a color bar but with fixed values, that I want to specify. use scale_fill_manual How I can do those two? p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=c(red, blue, green, purple, orange, pink, tan, violet, yellow)) Best, Ista Before is some code what I have tried so far. Regards Alex DataToPlot-matrix(data=seq(1:9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) tdm - melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster() + scale_fill_discrete() [[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.
Re: [R] ggplot2 customizing a plot
Hi, On Thu, Feb 21, 2013 at 4:12 AM, Alaios ala...@yahoo.com wrote: Hello Ista, I would like to thank you for your reply! Your code is indeed an improvement. This is my code now and there are two things still missing. DataToPlot-matrix(data=runif(9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) cols-colours() cols-cols[1:(nrow(DataToPlot)*ncol(DataToPlot))] tdm-melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=cols,breaks=c(1,0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1,0)) value looks like numbers, why are you converting it to a factor? My values go from 0 to 1 (might go slightly over the limits) and I want to specify one color for the following ranges, 1, 0.9,0.8,.,0 . That means that values between the intervals will be categorized based on their closest match. I don't really understand this. What I also tried is to create a gray scale pallete as this is printer friendly so the values from 0.9 to 0.1 get a greyish tone but I failed to do that with colours. How about ggplot(tdm, aes(x = Var2, y = Var1, fill = value)) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_gradient(low=gray90, high=black) + theme_bw() Could you please help me have both a. A fixed scale where values are categorized there and Value is numeric, and trying to treat it like a category is only going to make things difficult. b. a greyish pallete for the categories? Use scale_fill_gradient with different shades of gray as the low and high values, as shown above. Best, Ista I would like to thank you in advance for your reply Regards Alex From: Ista Zahn istaz...@gmail.com To: Alaios ala...@yahoo.com Cc: R help R-help@r-project.org Sent: Wednesday, February 20, 2013 4:54 PM Subject: Re: [R] ggplot2 customizing a plot Hi, On Wed, Feb 20, 2013 at 9:33 AM, Alaios ala...@yahoo.com wrote: Dear all, I want some help improve my ggplot as following: Make the plottable area with grid, so is easy one to see where each box refers to x and y values. I don't think you can easily move the grid to the front, but you can make the tiles transparent so the grid can be seen through them by setting the alpha 1. Add a color bar but with fixed values, that I want to specify. use scale_fill_manual How I can do those two? p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=c(red, blue, green, purple, orange, pink, tan, violet, yellow)) Best, Ista Before is some code what I have tried so far. Regards Alex DataToPlot-matrix(data=seq(1:9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) tdm - melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster() + scale_fill_discrete() [[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] ggplot2 customizing a plot
Let me try to explain this then. I have numbers like DataToPlot 4 5 6 1 0.4454995 0.4462009 0.4286807 2 0.3761550 0.5423205 0.6500785 3 0.3779496 0.4671437 0.1799601 and I want to have a color legend with each color that is mapped to the following printed values 1,0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1,0 For making life easier I have rounded up my number to one digit so matrixToPlot-matrix(data=round(matrixToPlot,digits=1),nrow=nrow(matrixToPlot),ncol=ncol(matrixToPlot),dimnames=list(yLabel, xLabel)) matrixToPlot 1 2 3 1 0.4 0.4 0.4 2 0.4 0.5 0.7 3 0.4 0.5 0.2 that indeed helps and makes the legend bar print the right values BUT there are not all the ranges printed there. So for the given example data set only the 0.2, 0.3,0.4,0.5,0.6,0.7 are printed with the 0,0.1,0.8,0.9,1 missing. Also I need some help to specify specific color to each of the given categories/ranges in the colorbar my code now looks like library(reshape2) library(ggplot2) matrixToPlot-matrix(data=runif(9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) matrixToPlot-matrix(data=round(matrixToPlot,digits=1),nrow=nrow(matrixToPlot),ncol=ncol(matrixToPlot),dimnames=list(seq(1:3), seq(4:6))) tdm - melt(matrixToPlot) cols-colours() cols-cols[1:(nrow(matrixToPlot)*ncol(matrixToPlot))] p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_discrete(h.start=1) + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0)) Regards Alex From: Ista Zahn istaz...@gmail.com Cc: R help R-help@r-project.org Sent: Thursday, February 21, 2013 2:15 PM Subject: Re: [R] ggplot2 customizing a plot Hi, Hello Ista, [[elided Yahoo spam]] Your code is indeed an improvement. This is my code now and there are two things still missing. DataToPlot-matrix(data=runif(9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) cols-colours() cols-cols[1:(nrow(DataToPlot)*ncol(DataToPlot))] tdm-melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=cols,breaks=c(1,0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1,0)) value looks like numbers, why are you converting it to a factor? why this is how I found I should solve the problem.. My values go from 0 to 1 (might go slightly over the limits) and I want to specify one color for the following ranges, 1, 0.9,0.8,.,0 . That means that values between the intervals will be categorized based on their closest match. I don't really understand this. What I also tried is to create a gray scale pallete as this is printer friendly so the values from 0.9 to 0.1 get a greyish tone but I failed to do that with colours. How about ggplot(tdm, aes(x = Var2, y = Var1, fill = value)) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_gradient(low=gray90, high=black) + theme_bw() Could you please help me have both a. A fixed scale where values are categorized there and Value is numeric, and trying to treat it like a category is only going to make things difficult. b. a greyish pallete for the categories? Use scale_fill_gradient with different shades of gray as the low and high values, as shown above. Best, Ista I would like to thank you in advance for your reply Regards Alex From: Ista Zahn istaz...@gmail.com Cc: R help R-help@r-project.org Sent: Wednesday, February 20, 2013 4:54 PM Subject: Re: [R] ggplot2 customizing a plot Hi, Dear all, I want some help improve my ggplot as following: Make the plottable area with grid, so is easy one to see where each box refers to x and y values. I don't think you can easily move the grid to the front, but you can make the tiles transparent so the grid can be seen through them by setting the alpha 1. Add a color bar but with fixed values, that I want to specify. use scale_fill_manual How I can do those two? p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=c(red, blue, green, purple, orange, pink, tan, violet, yellow)) Best, Ista Before is some code what I have tried so far. Regards Alex DataToPlot-matrix(data=seq(1:9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) tdm - melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster() + scale_fill_discrete
Re: [R] ggplot2 customizing a plot
Hi, On Thu, Feb 21, 2013 at 9:21 AM, Alaios ala...@yahoo.com wrote: Let me try to explain this then. I have numbers like DataToPlot 4 5 6 1 0.4454995 0.4462009 0.4286807 2 0.3761550 0.5423205 0.6500785 3 0.3779496 0.4671437 0.1799601 and I want to have a color legend with each color that is mapped to the following printed values 1,0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1,0 Are these numbers or not? Is .1 .2 3 etc.? If the answer is yes then I would use a continuous color scale. If not then I would use something besides numbers to represent the categories. For making life easier I have rounded up my number to one digit so OK, but it's still a number no? matrixToPlot-matrix(data=round(matrixToPlot,digits=1),nrow=nrow(matrixToPlot),ncol=ncol(matrixToPlot),dimnames=list(yLabel, xLabel)) matrixToPlot 1 2 3 1 0.4 0.4 0.4 2 0.4 0.5 0.7 3 0.4 0.5 0.2 that indeed helps and makes the legend bar print the right values BUT there are not all the ranges printed there. So for the given example data set only the 0.2, 0.3,0.4,0.5,0.6,0.7 are printed with the 0,0.1,0.8,0.9,1 missing. Because your data does not have values of 0, .01, .08, .09, or 1! If value is a number than these non-existent values are meaningful, but if it is categorical they are not. So if want these values treat value as numeric. Also I need some help to specify specific color to each of the given categories/ranges in the colorbar Earlier you said you wanted grayscale. Is that still true? If so either treat value as continuous and use scale_fill_gradient() as I suggested earlier, or treat is as categorical and use scale_fill_grey() my code now looks like library(reshape2) library(ggplot2) matrixToPlot-matrix(data=runif(9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) matrixToPlot-matrix(data=round(matrixToPlot,digits=1),nrow=nrow(matrixToPlot),ncol=ncol(matrixToPlot),dimnames=list(seq(1:3), seq(4:6))) tdm - melt(matrixToPlot) cols-colours() cols-cols[1:(nrow(matrixToPlot)*ncol(matrixToPlot))] p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_discrete(h.start=1) + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0)) I still don't see what is wrong with my earlier suggestion. If you want labels at intervals of .1 you can use p- ggplot(tdm, aes(x = Var2, y = Var1)) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0)) p + geom_raster(aes(fill=value), alpha=.5) + scale_fill_gradient(low=black, high=gray90, breaks=seq(0,1, .1)) If you don't like that solution please explain why! If you really want to specify the colors yourself you can go to all the trouble of dum.dat - data.frame(Var1=1, Var2=1, value=factor(seq(0, 1, .1))) p + geom_point(aes(fill=value), size=0, data=dum.dat) + geom_raster(aes(fill=factor(value)), alpha=.5) + scale_fill_manual(values = paste(gray, seq(20, 100, by=8), sep=)) but a) now you are fighting with ggplot instead of taking advantage of it, and b) I fail to see how this is an improvement. Best, Ista Regards Alex From: Ista Zahn istaz...@gmail.com To: Alaios ala...@yahoo.com Cc: R help R-help@r-project.org Sent: Thursday, February 21, 2013 2:15 PM Subject: Re: [R] ggplot2 customizing a plot Hi, On Thu, Feb 21, 2013 at 4:12 AM, Alaios ala...@yahoo.com wrote: Hello Ista, I would like to thank you for your reply! Your code is indeed an improvement. This is my code now and there are two things still missing. DataToPlot-matrix(data=runif(9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) cols-colours() cols-cols[1:(nrow(DataToPlot)*ncol(DataToPlot))] tdm-melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=cols,breaks=c(1,0.9,0.8,0.7,0.6,0.5,0.4,0.3,0.2,0.1,0)) value looks like numbers, why are you converting it to a factor? why this is how I found I should solve the problem.. My values go from 0 to 1 (might go slightly over the limits) and I want to specify one color for the following ranges, 1, 0.9,0.8,.,0 . That means that values between the intervals will be categorized based on their closest match. I don't really understand this. What I also tried is to create a gray scale pallete as this is printer friendly so the values from 0.9 to 0.1 get a greyish tone but I failed to do that with colours. How about ggplot(tdm, aes(x = Var2, y = Var1, fill = value)) + labs(x = MHz, y = Threshold, fill = Duty Cycle
Re: [R] ggplot2 customizing a plot
Hi, On Wed, Feb 20, 2013 at 9:33 AM, Alaios ala...@yahoo.com wrote: Dear all, I want some help improve my ggplot as following: Make the plottable area with grid, so is easy one to see where each box refers to x and y values. I don't think you can easily move the grid to the front, but you can make the tiles transparent so the grid can be seen through them by setting the alpha 1. Add a color bar but with fixed values, that I want to specify. use scale_fill_manual How I can do those two? p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster(alpha=.5) + scale_fill_manual(values=c(red, blue, green, purple, orange, pink, tan, violet, yellow)) Best, Ista Before is some code what I have tried so far. Regards Alex DataToPlot-matrix(data=seq(1:9),nrow=3,dimnames=list(seq(1,3),seq(4,6))) require(reshape) require(ggplot2) require(raster) tdm - melt(DataToPlot) p- ggplot(tdm, aes(x = Var2, y = Var1, fill = factor(value))) + labs(x = MHz, y = Threshold, fill = Duty Cycle) + geom_raster() + scale_fill_discrete() [[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.
