Question

HOW to define the "parLabVc" indices in ropls package.

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yuan.guo001 • 0

@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 • 1.7k views

ADD COMMENT • link updated 6.5 years ago by etienne.thevenot ▴ 40 • written 6.5 years ago by yuan.guo001 • 0

score 0 · Answer 1 · 2018-05-15

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etienne.thevenot ▴ 40

@etiennethevenot-8285

Last seen 22 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")

ADD COMMENT • link 6.5 years ago etienne.thevenot ▴ 40

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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

ADD REPLY • link 6.5 years ago yuan.guo001 • 0

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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"]]))))