`PlotSignatureTransformed()`: Removed `vst` from the default transforms parameter

[LotharukpongJS]

Dear Hajk,

I think PlotSignatureTransformed() should run with the default installation of myTAI without DESeq2.

However, PlotSignatureTransformed() had vst as one of the transformations as a default, i.e. transforms = c("none", "log2", "sqrt", "vst", "rank", "squared"). Since, vst is from the DESeq2 package and in case DESeq2 is not installed or doesn't satisfy DESeq2 (>= 1.29.15), then the function will not work.

The default parameters are now.

PlotSignatureTransformed <-
  function(ExpressionSet,
           measure            = "TAI",
           TestStatistic      = "FlatLineTest",
           transforms         = c("none", "sqrt", "log2", "rank", "squared"),
           modules            = NULL,
           permutations       = 1000,
           pseudocount        = 1,
           p.value            = TRUE,
           shaded.area        = FALSE,
           xlab               = "Ontogeny",
           ylab               = "Transcriptome Index",
           main               = "",
           lwd                = 4,
           alpha              = 0.1,
           y.ticks            = 3)

However, the issue of ks.test.default warning messages for TestStatistic = "FlatLineTest" remains.

Best, Sodai

[LotharukpongJS]

If I may add another point, I think the README.md should say libomp rather than lomp.

https://github.com/drostlab/myTAI/blob/46eb92798755ac2e9c1a80a40f3d3ab2fa19037d/README.md?plain=1#L33-L38

to

brew install llvm libomp
cd /usr/local/lib
ln -s /usr/local/opt/libomp/lib/libomp.dylib ./libomp.dylib

This may have come from https://github.com/drostlab/myTAI/pull/26. It seems like lomp doesn't exist and is a spelling mistake.

$ brew install lomp
==> Downloading https://formulae.brew.sh/api/formula.jws.json

==> Downloading https://formulae.brew.sh/api/cask.jws.json

Warning: No available formula with the name "lomp". Did you mean libomp?
==> Searching for similarly named formulae and casks...
==> Formulae
libomp ✔

To install libomp ✔, run:
  brew install libomp ✔

==> Casks
loom

To install loom, run:
  brew install --cask loom

[HajkD]

Excellent points! I fully agree and merged now.

Many thanks, Hajk