When plotting a PLS-DA object with plotLoadings, the genes are colored according to the outcome of interest. This is a very interesting information, but when I extract the values with selectVar, I can’t find a way of also getting the group of interest.
Is there a way of getting this information?
Using the below code as an example:
suppressMessages(library(mixOmics))
data(srbct)
X <- srbct$gene
Y <- srbct$class
model <- plsda(X, Y)
l <- plotLoadings(model, contrib = "max")
head(l)
#> EWS BL NB RMS Contrib.EWS Contrib.BL
#> g937 -0.5603682 1.347079 0.8186230 -0.3855818 FALSE TRUE
#> g1894 -0.5572560 1.112754 0.9372550 -0.3666102 FALSE TRUE
#> g74 -0.4260267 1.841357 0.3642796 -0.4651797 FALSE TRUE
#> g1932 -0.3446706 1.467506 0.6792611 -0.5981877 FALSE TRUE
#> g1884 -0.3383005 2.007751 0.2094040 -0.5396972 FALSE TRUE
#> g571 -0.4856335 1.016801 0.9521337 -0.4195219 FALSE TRUE
#> Contrib.NB Contrib.RMS Contrib GroupContrib color importance
#> g937 FALSE FALSE FALSE BL #F68B33 0.05769917
#> g1894 FALSE FALSE FALSE BL #F68B33 0.05561153
#> g74 FALSE FALSE FALSE BL #F68B33 0.05506304
#> g1932 FALSE FALSE FALSE BL #F68B33 0.05406453
#> g1884 FALSE FALSE FALSE BL #F68B33 0.05360364
#> g571 FALSE FALSE FALSE BL #F68B33 0.05301618
Created on 2022-08-01 by the reprex package (v2.0.1)
sessioninfo::session_info()
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Therefore, rather than using selectVar() just take the output of plotLoadings() directly! You can find what you’re after in the GroupContrib column of the output.
Hope this helped
That’s was It, thank you very much!!