Heatmap without levelplot

Hi Uwe,

thanks a lot for your answer! And thanks a lot to all others helping me 
with this issue!

Uwe Ligges schrieb:

Antje wrote:

Hi Uwe,

I tried to explain my problem with the given example.
I don't see any documentation which tells me that the length of 
"col.regions" should be one less than "at". (At least I assume now 
that it should be this way...)
If it's equal or longer some colors (in the middle of the 
color-vector) are simply not used.
Just try the example below with rainbow(5) and rainbow(6) and compare 
the results... both plot will use 5 colors!
Sorry, but this behaviour is not really self-explaining to me... 
maybe I'm to blind to find the documentation which says that only one 
color less will ensure the usage of all colors.

Well, of you have 5 at locations (i.e. breaks), then you have 4 
intervals in between and that's the amount of colors that is sensible.

 From the documentation this was not really clear to me (though it makes 
sense, I agree)

(It is so important for me because I need to display a heatmap with 
colors let's say
* all lower data outliers "green",
* all higher data outliers "blue" and
* everything else within the color range "yellow" to "red".
I've seen that some values do not get blue or green though they are 
outliers...
I've attached one graph, I've generated - maybe it helps to understand)

Any wrong assumption?

Maybe:

Say you want everything below -1 be considered as a lower outlier and 
all above 1 is a higher outlier, then you can say:


levelplot(matrix(c(1,2,0,-2), nrow=2),
    at = c(-Inf, seq(-1, 1, length=10), Inf),
    col.regions = c(rgb(0,1,0),
         hcl(seq(20, 80, length=10), c=400),
         rgb(0,0,1)))

Then below -1 is green (rgb(0,1,0)), above 1 is blue (rgb(0,0,1)) and 
in between we have 10 regions from -1 to 1 each with a color between 
some kind of yellow and red in hcl() space.

Thank you for this little example. Just two comments:

1) I was not aware of the possibility to use "Inf" - it just has the 
disadvantage that these colors are not displayed at the color vector 
(maybe this can be adjusted somehow)

2) if you replace one number of the matrix with -1, it will be displayed 
green.
So it would be considered as an outlier. From the documentation it was 
also not clear to me that the lower endpoint of the interval is always 
excluded (except for the very first value of the at-vector), while the 
upper endpoint will be included. (This also makes sense but in this case 
I have to slightly modify my data because I'd like to include both 
endpoints of my non-outlier-range...)

Anyway, I guess, I solved all problems and found a workable solution :-)

Ciao,
Antje

Uwe Ligges

Ciao,
Antje


Uwe Ligges schrieb:

Antje wrote:

Hi there,

as I'm not sure to understand the coloring levelplot uses, I'm 
looking for another easy way to create a heatmap like this:

library(lattice)
mat <- matrix(seq(1,5, length.out = 12), nrow = 3)
mat[1,2] <- 3.5

my.at <- seq(0.5,5.5, length.out = 6)
my.col.regions <- rainbow(5)

graph <- levelplot(t(mat[nrow(mat):1, ] ), at = my.at, col.regions 
= my.col.regions)
print(graph)

Can anybody help me with some hints or little examples?

Dear Antje,

since you are asking the same question again now, maybe you can 
explain what you are going to get? In fact, I do not undertsand 
where your problem is. R places the colors according to the values 
in your matrix very well including the legend and I thought up to 
today that the plot is self explaining.

Best wishes,
Uwe Ligges

Antje