PCAtools - change colour of points
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0
Entering edit mode
Terra • 0
@terra-24154
Last seen 7 months ago

Hi,

I'm running PCAtools on a cancer and control samples with this code:

bp1 <- PCAtools::biplot(pcaobj = PCA,
                   colby = 'group',
                   colkey = c(control = 'blue', cancer = 'pink'),
                   legendPosition = "right",
                   lab = NULL, 
                   hline = 0, vline = 0)

        geom_point(shape = 1,size = 3,colour = "black") +

        theme(legend.title = element_blank(),
              legend.position=c(0.9,0.9),
              legend.background = element_rect(fill="white", size=.5, linetype="dotted"),
              legend.box.background = element_rect(colour = "black"))

The error I'm getting is: Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.

Running the above code I get the plots, but they're just empty circles, however if I comment out colkey I'll get the default colours. I'm not sure what I'm doing wrong here.

sessionInfo( )

R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

PCAtools • 247 views
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2
Entering edit mode
@kevin
Last seen 38 minutes ago
Republic of Ireland

One of the ideas behind PCAtools is that one does not require extra ggplot2 'add on' functions, like you are using:

geom_point(shape = 1,size = 3,colour = "black") +

        theme(legend.title = element_blank(),
              legend.position=c(0.9,0.9),
              legend.background = element_rect(fill="white", size=.5, linetype="dotted"),
              legend.box.background = element_rect(colour = "black"))

You can apply the same functionality via parameters that are passed to biplot()

Irrespective, in your code, there is no plus sign ('+') to link biplot() with these extra functions.

The message that you receive is a warning message, I believe, not an error message. Can you please confirm that control and cancer are part of your metadata column called group?

Kevin

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Entering edit mode

Hi,

Thank you! I feel so silly, my columns weren't control and cancer I had labelled them as something else. It works now, much appreciated.

Perfect, I'll adapt my code so I can omit using ggplot2, it was a bit of a rushed attempt at getting the graph to appear how I wanted it.

Thank you again!

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