feature request: ggplot for plotLoadings

[samuelmontgomery]

Hi,

Just wondering if it would be possible to output the plotLoadings function as a ggplot object?
Currently it uses base R within the plotLoadings_barplot function to plot a barplot, which makes it more difficult to customise and is resulting in the feature names for some of my plots being cut off on the right axis if they're too long

Both the plotIndiv and plotVar are already output as ggplot objects so it would also make it uniform across those plots

Thanks!

[evaham1]

Hi @samuelmontgomery I agree a ggplot output would be much better, I will look into implementing this in the next couple of weeks

[samuelmontgomery]

Thanks - I have made a workaround function for the moment that uses the plotLoadings output to replot using ggplot (only for splsda at the moment!)

ggloadingplot <- function(object,
comp,
method = 'median',
contrib = 'max',
size.name = 0.8,
ndisplay = 20,
title)
{
loading_plot <- plotLoadings(object,
comp = comp,
block = "X",
method = method,
contrib = contrib,
size.name = size.name,
legend = T,
ndisplay = ndisplay,
title = title,
size.title = 1.5,
xlim = c(-0.8, 0.8))

loading_plot <- as.data.frame(loading_plot$X)
loading_plot$component <- factor(rownames(loading_plot), levels = rownames(loading_plot)[order(-abs(loading_plot$importance))])

p <- ggplot(loading_plot, aes(x = component, y = importance, fill = GroupContrib)) +
geom_bar(stat = "identity") +
scale_fill_manual(values = setNames(unique(loading_plot$color), unique(loading_plot$GroupContrib))) +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
coord_flip() +
labs(y = "Importance", x = NULL, title = title, fill = "Outcome")
return(p)
}