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YoannPa / methview.qc

HM450.QCView allows you to generate quality control plots from your Human Methylation 450K dataset.
GNU General Public License v3.0
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sampleQC.biplot() PCA function error #3

Closed AnjaCaRa closed 3 years ago

AnjaCaRa commented 3 years ago

The following function is currently only returning an error:

sampleQC.biplot(RnBSet = result, PCx =1, PCy=2, loadings=TRUE, loadings.col="blue", point.size=2.5, color.data="PID", shape.data=NULL) Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column

YoannPa commented 3 years ago

Hi, I haven't been able to reproduce your error with the latest version of methview.qc. However your code was returning other errors, which I fixed.

One error was linked to the fact that the legend was too big for the viewport: Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), : Viewport has zero dimension(s) If you come to experience this error, just manually increase the plotting panel within the RStudio interface, and execute the function again.

As a general advice: when defining legends for colors or shapes, it is better to a small amount of possible values. otherwise the legend becomes too big, the colors are too similar, and the interpretation of the plot becomes impossible to the human eye.

Please install the latest version of methview.qc from Github, try again the function, and let me know if it works.

AnjaCaRa commented 3 years ago

Thank you very much, the plotting is working now!

YoannPa commented 3 years ago

Great ! I close the issue.