slplot fails if called inside a function

[StuntsPT]

Dear pcaMethods team,

While teaching a class last week we have realized that slplot will fail if called from inside a function with the error:

Error in plot.xy(xy, type, ...) : object '<object_name used as argument for "scol">' not found 

I'm not sure this is a bug in pcaMethods or something more general to R. But I thought I should provide you with a 'heads up' nontheless.

Below is a minimal example you can use for reproducing the issue:

library(pcaMethods)

wine <- read.csv("http://archive.ics.uci.edu/ml/machine-learning-databases/wine/wine.data", sep=",")

# Add column names
colnames(wine) <- c("Cultivar", "Alcohol", "Malic acid", "Ash",
                    "Alcalinity of ash", "Magnesium", "Total phenols",
                    "Flavanoids", "Nonflavanoid phenols", "Proanthocyanins",
                    "Color intensity", "Hue", "OD280/OD315 of diluted wines",
                    "Proline")

# The first column corresponds to the cultivar class
cultivar_classes <- factor(wine[,"Cultivar"])

winePCAmethods = pca(wine[,-1], scale="vector", center=T, nPcs=2, method="svd")

# Plot it
slplot(winePCAmethods,
       scol=cultivar_classes,
       scoresLoadings=c(TRUE,FALSE))

legend("bottomright", legend = c("Cv1","Cv2","Cv3"), pch = 1,
       col = c("black","red","green"))

slplot(winePCAmethods,
       scoresLoadings=c(FALSE,TRUE))

### The above part works just fine. Below is where the problem lies:

my_broken_function = function(current_data, current_classes) {
  
  my_PCAmethods = pca(current_data[,-1], scale="vector", center=T, nPcs=2, method="svd")
  
  # Plot it
  slplot(my_PCAmethods,
         scol=current_classes,
         scoresLoadings=c(TRUE,FALSE))
  
  legend("bottomright", legend = c("Cv1","Cv2","Cv3"), pch = 1,
         col = c("black","red","green"))
}

my_broken_function(wine, cultivar_classes)

In short, if slplot is called from inside a function, the argument for scol cannot be found.

We thought it would be helpful to report. If any further information is required, feel free to ask away.

[hredestig]

Hi, Thanks for the info and excellent bug report, slplot was mainly meant as a quick way to plot results in an interactive session. But that's no excuse for the inelegant failure. I'll have a look.