[R] ggplot2 customizing a plot
Ista Zahn
istazahn at gmail.com
Thu Feb 21 16:24:39 CET 2013
Hi,
On Thu, Feb 21, 2013 at 9:21 AM, Alaios <alaios at 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 <istazahn at gmail.com>
> To: Alaios <alaios at yahoo.com>
> Cc: R help <R-help at 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 <alaios at 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") +
> 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 <istazahn at gmail.com>
>> To: Alaios <alaios at yahoo.com>
>> Cc: R help <R-help at 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 <alaios at 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]]
>>>
>>>
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>>
>>
>
>
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