adjusting color and alpha in plot.mtpc

[maria]

Hi Chris, 

I‘m doing some fine tuning for final plots generated from your braingraph package for a publication. The editorial office asked me to reproduce the mtpc plots in a colorblind friendly way. 

Is there a way to adjust the colors? The usual ggplot scale_color commands don´t seem to work. Also is there a way to adjust the alpha and size of the null stat points? 

Thank you!

Maria

[Chris Watson]

Unfortunately the only easy way is for you to edit "plot.mtpc" for your purpose. I should probably make a global option to allow for this kind of thing but I don't know when I'll be able to get around to it.

To edit it you would have to either clone the GitHub repository, edit "mtpc.R", and source that file; or run "plot.mtpc <- edit(brainGraph:::plot.mtpc)" and edit from within the R console.

* For the observed data: in the code you will see that the color "red4" is used several times, so you can find & replace for that string. You can also see where "alpha" is used (variously set to 0.3 or 0.4).

* For the null points: you can change "darkgreen" to whatever you want. To change the size you will have to add a "size=X" to the function call and replace "X" with the number you want. Set it to something smaller than 1 to make the points smaller. This line of code occurs where it says "if (isTRUE(show.null))"

These are all in the "plot_single" local function (local to "plot.mtpc") if you have ggplot2 installed.

Please let me know if you run into any issues.

Chris

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[Maria Feldmann]

Works perfectly, thank you so much!

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