All, I frequently make spreadsheets in Excel in which I rank values in columns by stop-light colors (red is bad, yellow is OK, green is good). Image and heatmap expect a matrix in which all the data are in the same scale, but I frequently have different scales in different columns. ie. Column one runs from 1-10 while column 2 runs from 1-100. I thus need to define a separate color ramp for each column. In addition, sometimes the smaller numbers are colored green, while sometimes the larger numbers are preferred and colored green. I also want to print in each cell the numeric value, and I need to show row names. A crude example without the color: RowNames Col1 Col2 ---------------------------------------------- Row1 1 1 Row2 5 50 Row3 7.5 80 Row4 10 99 ...... Is there any R package that can do something similar? Can I create a plot that is a matrix of rectangles and get color and text that way? Any help is greatly appreciated. Thanks, John [[alternative HTML version deleted]]
Hi, John- Would it be possible to scale the values in each column to fall between 0 and 1 (or standardize them) and use a single color ramp? Ken On 02/14/12, John Nicholas wrote:> All, > > I frequently make spreadsheets in Excel in which I rank values in columns > by stop-light colors (red is bad, yellow is OK, green is good). > > Image and heatmap expect a matrix in which all the data are in the same > scale, but I frequently have different scales in different columns. ie. > Column one runs from 1-10 while column 2 runs from 1-100. I thus need to > define a separate color ramp for each column. In addition, sometimes the > smaller numbers are colored green, while sometimes the larger numbers are > preferred and colored green. I also want to print in each cell the numeric > value, and I need to show row names. A crude example without the color: > > RowNames Col1 Col2 > ---------------------------------------------- > Row1 1 1 > Row2 5 50 > Row3 7.5 80 > Row4 10 99 > ...... > > Is there any R package that can do something similar? Can I create a plot > that is a matrix of rectangles and get color and text that way? > > Any help is greatly appreciated. > > Thanks, > > John > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.
Hi, John- Sorry if my last email was not clear.? In R I imagine you having two matrices. One with the raw values and one with values scaled or standardized by column. The matrix with the values scaled by column is used to make the heatmap (i.e. color the image) and the matrix with the raw values is then overlaid on the heatmap. The details of the image or heatmap functions escape me as I have not worked with them for several years. Without doing this myself (and without a lot of time to try it out), I cannot speak for its difficulty, although I don't imagine it being too tedious. It is likely that others will have good ideas and I have copied this back to the list to hopefully find out... Ken ? ? ? On 02/14/12, John Nicholas wrote:> I can do that for the color ramp (although a bit tedious to do for each new spreadsheet), but then how do I get the actual values printed in the cells? > > > > > > On Tue, Feb 14, 2012 at 2:35 PM, Kenneth Frost <kfrost at wisc.edu <kfrost at wisc.edu>> wrote: > > > > > Hi, John- > > > > > Would it be possible to scale the values in each column to fall between 0 and 1 (or standardize them) and use a single color ramp? > > > > > Ken > > > > > > > > > > On 02/14/12, John Nicholas ? wrote: > > > > > > All, > > > > > > > > > > > > I frequently make spreadsheets in Excel in which I rank values in columns > > > > > > by stop-light colors (red is bad, yellow is OK, green is good). > > > > > > > > > > > > Image and heatmap expect a matrix in which all the data are in the same > > > > > > scale, but I frequently have different scales in different columns. ie. > > > > > > Column one runs from 1-10 while column 2 runs from 1-100. I thus need to > > > > > > define a separate color ramp for each column. In addition, sometimes the > > > > > > smaller numbers are colored green, while sometimes the larger numbers are > > > > > > preferred and colored green. I also want to print in each cell the numeric > > > > > > value, and I need to show row names. A crude example without the color: > > > > > > > > > > > > RowNames ? ? ? ?Col1 ? ? Col2 > > > > > > ---------------------------------------------- > > > > > > Row1 ? ? ? ? ? ? ? ? ? 1 ? ? ? ? ?1 > > > > > > Row2 ? ? ? ? ? ? ? ? ? 5 ? ? ? ? 50 > > > > > > Row3 ? ? ? ? ? ? ? ? ?7.5 ? ? ? 80 > > > > > > Row4 ? ? ? ? ? ? ? ? ?10 ? ? ? ?99 > > > > > > ...... > > > > > > > > > > > > Is there any R package that can do something similar? Can I create a plot > > > > > > that is a matrix of rectangles and get color and text that way? > > > > > > > > > > > > Any help is greatly appreciated. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > John > > > > > > > > > > > > > > > > ? ? ? [[alternative HTML version deleted]] > > > > > > > > > > > > ______________________________________________ > > > > > > R-help at r-project.org <R-help at 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. > > > > > > > > > > > > > > >
Check out the XLConnect package for formatting a spreadsheet. On Tue, Feb 14, 2012 at 5:21 PM, John Nicholas <jbnichola at gmail.com> wrote:> All, > > I frequently make spreadsheets in Excel in which I rank values in columns > by stop-light colors (red is bad, yellow is OK, green is good). > > Image and heatmap expect a matrix in which all the data are in the same > scale, but I frequently have different scales in different columns. ie. > Column one runs from 1-10 while column 2 runs from 1-100. I thus need to > define a separate color ramp for each column. In addition, sometimes the > smaller numbers are colored green, while sometimes the larger numbers are > preferred and colored green. I also want to print in each cell the numeric > value, and I need to show row names. A crude example without the color: > > RowNames ? ? ? ?Col1 ? ? Col2 > ---------------------------------------------- > Row1 ? ? ? ? ? ? ? ? ? 1 ? ? ? ? ?1 > Row2 ? ? ? ? ? ? ? ? ? 5 ? ? ? ? 50 > Row3 ? ? ? ? ? ? ? ? ?7.5 ? ? ? 80 > Row4 ? ? ? ? ? ? ? ? ?10 ? ? ? ?99 > ...... > > Is there any R package that can do something similar? Can I create a plot > that is a matrix of rectangles and get color and text that way? > > Any help is greatly appreciated. > > Thanks, > > John > > ? ? ? ?[[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.-- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it.
A minimum code to plot a coloured matrix with text labels could be the
following:
library(grid)
library(scales)
library(RColorBrewer)
diverging_palette <- function(d = NULL, centered = FALSE, midpoint = 0,
colors = brewer.pal(7,"PRGn")){
half <- length(colors)/2
if(!length(colors)%%2) stop("requires odd number of colors")
values <- if(centered) {
low <- seq(min(d), midpoint, length=half)
high <- seq(midpoint, max(d), length=half)
c(low[-length(low)], midpoint, high[-1])
} else {
mabs <- max(abs(d - midpoint))
seq(midpoint-mabs, midpoint + mabs, length=length(colors))
}
gradient_n_pal(colors, values = values)
}
matrixGrob <- function(d){
nc <- ncol(d)
nr <- nrow(d)
palet <- diverging_palette(d, center=FALSE)
fill.matrix <- palet(d)
dim(fill.matrix) <- dim(d)
## matrix of square tiles
rg <- rasterGrob(fill.matrix, width=unit(1, "npc"),
height=unit(1,
"npc"), interpolate = FALSE)
## position of the labels
xy <- expand.grid(y = rescale(seq_len(nr), c(0.5/nr, 1 - 0.5/nr) ),
x = rescale(seq_len(nc), c(0.5/nc, 1 - 0.5/nc))
)
## text
tg <- textGrob(label=round(d, 3), x=xy$x, y= 1 - xy$y, def="npc")
gTree(children=gList(rg, tg))
}
grid.matrix <- function(d)
grid.draw(matrixGrob(d))
d <- cbind(x=rnorm(10), y=rnorm(10))
grid.newpage()
grid.matrix(d)
I don't think it would be very hard to adapt to your needs, basically
you need to add rownames on top, apply() the scale to each column
independently (as opposed to the full matrix at the moment) and
combine the results in a fill.matrix. Having one colour scale across
the matrix makes more sense, imho.
HTH,
b.
On 15 February 2012 11:21, John Nicholas <jbnichola at gmail.com>
wrote:> All,
>
> I frequently make spreadsheets in Excel in which I rank values in columns
> by stop-light colors (red is bad, yellow is OK, green is good).
>
> Image and heatmap expect a matrix in which all the data are in the same
> scale, but I frequently have different scales in different columns. ie.
> Column one runs from 1-10 while column 2 runs from 1-100. I thus need to
> define a separate color ramp for each column. In addition, sometimes the
> smaller numbers are colored green, while sometimes the larger numbers are
> preferred and colored green. I also want to print in each cell the numeric
> value, and I need to show row names. A crude example without the color:
>
> RowNames ? ? ? ?Col1 ? ? Col2
> ----------------------------------------------
> Row1 ? ? ? ? ? ? ? ? ? 1 ? ? ? ? ?1
> Row2 ? ? ? ? ? ? ? ? ? 5 ? ? ? ? 50
> Row3 ? ? ? ? ? ? ? ? ?7.5 ? ? ? 80
> Row4 ? ? ? ? ? ? ? ? ?10 ? ? ? ?99
> ......
>
> Is there any R package that can do something similar? Can I create a plot
> that is a matrix of rectangles and get color and text that way?
>
> Any help is greatly appreciated.
>
> Thanks,
>
> John
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.