PCAtools lables missing or out of the plot
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luca.s ▴ 10
@lucas-24386
Last seen 11 weeks ago
Italy

I am new to PCAtools, and I am trying to use it to perform PCA on log2cpm from edgeR and plotting the results. I am experiencing some issues with the plotting. In detail, when I try ti increase size of the points and/or of the lables, some of the lables go out of the plot or do not show up. Any suggestion? Version of the PCAtools is 1.0.0 run under R version 36.1 Thanks, Luca


#logcpm is the matrix with log2cpm data
#matadata is the datagrame with metadata, column of interest is 'type'
p <- pca(logcpm, metadata = metadata,removeVar = 0.9)

biplot(p,
colby = 'type',colkey = c('case' = 'salmon', 'control' = 'cyan3'),
hline = 0, vline = 0,
legendLabSize = 16, legendIconSize = 8.0,
gridlines.major = F,gridlines.minor = F,
pointSize = 10,
labSize=5,
drawConnectors = T,
legendPosition = 'right')
PCAtools • 187 views
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@kevin
Last seen 4 hours ago
Republic of Ireland

Hi,

You could increase the values of xlim and / or ylim

Note that EdgeR has the plotMDS() function, which allows one to perform multi-dimensional scaling.

Kevin

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Thanks Kevin, solved following your suggestion. PlotMDS is an option, but, for what I can menage, the aesthetics of the plot ar far less captivating than those obtained with PCAtools.

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