R help - Jul 2019 - How to set scale of color scatterplot points relative to a third variable?

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

	[[alternative HTML version deleted]]

Hi Sarah,
The size_n_color function in the plotrix package does something like
this. To get the colors that you want using "color.scale" in the same
package, look at the help page for that function. The values in
A1.matrix[,3] probably don't range from 0 to 2, so getting exactly
what you want can be a bit tricky with 1=white. If you can post a
representative sample of these values, it should be doable.

Jim

On Sat, Jul 6, 2019 at 2:56 AM Flaherty, Sarah (NIH/NCI) [F] via
R-help <r-help at r-project.org> wrote:
>
> 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
>
>         [[alternative HTML version deleted]]
>
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