When i run the below code of lines in R version 4.0.3 throws the below error message: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotPCA’ for signature ‘"prcomp"’

Code should be placed in three backticks as shown below

library(SMLoutliers)
library(plotly)
library(DESeq2)
library(ggplot2)
library(datasets)
library(BiocGenerics)
library(scatterplot3d)
library(plyr)
library(dplyr)
data(stiff)
#calculating Maha distance for Data 
mahaDistance<-mahalanobis(stiff,colMeans(stiff),var(stiff))
stiff$MahaDistance<- mahaDistance

stiff1<-arrange(stiff,desc(MahaDistance))

#identifying outliers (first 5 outliers)
stiff1$outliers<- c(rep("outlier",5),rep("not-outlier",nrow(stiff1)-5))
stiff1$outliers

#plotting outliers using PCA
pca_estudio<-prcomp(stiff1[,1:4], center = TRUE,scale. = FALSE)
ggplotly(plotPCA(pca_estudio,vectorVariables = c("x1","x2"),groups =stiff1$outliers))

This error is simply telling you that a prcomp object isn't a valid input for plotPCA. You can see what valid inputs are, using showMethods

> showMethods(plotPCA)
Function: plotPCA (package BiocGenerics)
object="DESeqTransform"

and further you can use the help page ?plotPCA, which says (after you choose the DESeq2 help page)

Description:

     This plot helps to check for batch effects and the like.

Usage:

     ## S4 method for signature 'DESeqTransform'
     plotPCA(object, intgroup = "condition", ntop = 500, returnData = FALSE)

Arguments:

  object: a 'DESeqTransform' object, with data in 'assay(x)', produced
          for example by either 'rlog' or
          'varianceStabilizingTransformation'.

You can plot the results from running prcomp directly, doing something like

plot(pca_estudio$x[,1:2])

And modifying to use different plotting symbols, etc