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rplotbeeswarm

How to set Individual colors in beeswarm (R)?

I want to plot some data using beeswarm in R, where the bg color of each point is defined by a column in my data. For example:

head(mydata)

## id   provean color
## 1635 9.428   #fee5d9
## 1092 9.000   #fb6a4a
## 791  8.708   #ffffff
## 1472 7.596   #fcae91
## 228  7.552   #ffffff
## 1004 7.433   #fcae91

The color column has the hex color codes I would like each point to have, and I try to implement it like this:

colorByMML <- mydata$color
beeswarm(mydata$provean,pch=21,cex=0.7, bty="n", col="#708090",pwbg=colorByMML)

But I get different colors than the expected ones. enter image description here

If instead of the hex codes I give integers, I get other colors. For instance if instead of the hex code of white(#ffffff) I input '1', I get black as the bg color. In short, how do I customize the color of each point?

Solution

  • Your code should work fine as it is, assuming colorByMML has type "character". However, if colorByMML has type "factor", the integer factor levels will be used (along with your default palette) to set colors. Based on the colors in your figure, I'm guessing this is the problem.

    In other words, this is probably what you are looking for:

    colorByMML <- as.character(mydata$color)