[R] How to set scale of color scatterplot points relative to a third variable?

[Flaherty, Sarah (NIH/NCI) [F]]

Hello Kind and Generous Volunteers,

I'm trying to use a scatter plot to visualize three variables: time, radius, and intensity. I would like each point on the scatterplot to be colored according to a gradient, in which red indicates an intensity less than 1, white indicates an intensity of 1, and green indicates an intensity more than 1.

```
#A1 scatter plot

colors <- c("firebrick2", "white", "darkolivegreen3")
class <- classIntervals(A1.matrix[,3], 10) #A1.matrix[,3] is "Intensity"
colorcode <- findColours(class, colors)
plot(A1.matrix[,1], A1.matrix[,2]) #A1.matrix[,1] is "Time" and A1.matrix[,2] is "Radius"
points(A1.matrix[,1], A1.matrix[,2], pch = 19, col = colorcode)

```

It is very close to what I am looking for. Firebrick2 and darkolivegreen3 correspond to the minimum and maximum values in A1.matrix[,3] respectively. But white does not correspond to 1. How can I set white equal to 1?


Ideally, the graph would also have a color bar scale to show what the min and max values are. I’ve read that findColours returns two attributes for use in constructing a legend, but I haven’t been able to find much more information than that.

I've had success doing something similar with a levelplot heatmap, using at=unique as shown below. However, I just copied that from somewhere online and it doesn't seem to work in the points function, I can’t find it using help() or google, and I'm not sure how it works or if it could somehow be applied. The colorbar scale is automatically part of the graph with levelplot.

```
#A1 heat map

levelplot(nbin.A1, cuts = 50, at= unique(c(seq(A1min,1, length = 100), seq(1,A1max, length=100))), col.regions = colorRampPalette(c("firebrick2", "white", "darkolivegreen3"))(1e3), xlab = "Radius (Microns)", ylab = "Time")

```

Thank you for reading! Your volunteer work is SO appreciated!!

Best,
Sarah Flaherty

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