Hi, every one.
I am currently working on a project using heat map. however, many heat map packages provided by R does not allow addition of a regression line to each cells. in my example, each cell represent a regression coefficient. does anyone know how t draw a heat map with regression line as an element? one example is shown in the enclosed figure.
If you're good with the base plotting functions in R, you can use line() and polygon() to plot each of these lines and bands. It's just a matter of finding the appropriate x- and y-values for the lines to go. I'm not sure if there's a built-in automatic way to do these.
Another option that might be easier would be to not technically use a heat map at all, but just use subplots (using the par() or layout() functions) to imitate a heat plot. Within a given subplot it will be very easy to plot the appropriate regression line, and you can set the subplot's background color to what you want. That seems like it would be reasonable in this case since, as far as I can tell, the rows and columns don't have an inherent order, so this isn't really a heat map so much as just a table of tiny plots.
many thanks for your help. however, there is dendrogram at the bottom of this plot. which method do you think is the best to also draw the dendrogram? I also attach the snapshot of the bottom.
thank you again for your answers.
I'm not sure about that as I've never done one. A dendrogram could still be done using the base plotting functions but it would be pretty hacky. It's possible that it might be easier to just make the subplots and regression lines in R and then add the dendrogram by hand in photoshop, GIMP, etc. (I could be wrong, though, there might be an easier built-in way of doing it, I'm just not aware of one since I've never tried to make a plot like this).
R is open source. So the code for drawing a heatmap is available. You can take this code and change it according to your needs.
Your needs seem somewhat special and it might take too much work and time to write R code that will produce a picture exactly as you want it (unless you will need it often!). You might be better off draing the elements separately and put them together using a graphics software (as Stephen suggested). You can use R to draw the colored rectangles ("rect") and use "lines" and "polygon" to add the regression lines inside the rectangles. The dendrogram could be drawn seperately. See "?dendrogram" for help on that.
A possibility to draw both, heatmap and dendrogram, in the same graphics window is by splitting the window using "split.screen" or "layout".
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