HOW to define the "parLabVc" indices in ropls package.
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@yuanguo001-15824
Last seen 6.5 years ago

Hi, I am using package"ropls" to generate PCA plot. And I want to change the  labels of observations on the plot, which is defaulted as the row name of m data set. 

But, I do not know how to define the labels ("indices of "x") that I want to display in my PCA plot. 

following the argument in the manual: 

"parLabVc,   Optional character vector for the labels of observations on the plot; default is NA [ie row names of ’x’, if available, or indices of ’x’, otherwise, will be used]"

R ropls • 1.6k views
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@etiennethevenot-8285
Last seen 21 months ago
France

Hi,

Below is an example of labels ("s1", "s2", ..., "sN"), where N is the total number of samples. You can use any character vector of length N. Does it answer your question?

Etienne.

> library(ropls)
> data(sacurine)

> pcaModel <- opls(sacurine[["dataMatrix"]])
> plot(pcaModel, parLabVc = paste0("s", 1:nrow(sacurine[["dataMatrix"]])), typeVc = "x-score")

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Hi Etienne,

thank you for your answer. My observations belong to 5 groups. Can I assign each group with symbols of "circles", "triangles" and so on, respectively? That will be more clean that just like"S1,S2,S3,S4......." on the plot

Thank you for your help.

Yuan

 

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You cannot use symbols (but special characters work). A better option would be to use colors according to your classes (use a factor in the parColFcVn argument):

> library(ropls)
> data(sacurine)
> pcaModel <- opls(sacurine[["dataMatrix"]])
> plot(pcaModel, typeVc = "x-score", parLabVc = paste0("S", 1:nrow(sacurine[["dataMatrix"]])), parAsColFcVn = as.factor(rep_len(paste0("G", 1:5), length.out = nrow(sacurine[["dataMatrix"]]))))

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It works. Thank you so much

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