I'm making PCA graphs for my expression data.
2D PCA are working fine with ggplot2 package.
I'm using scatterplot3d for 3D PCA, but keep getting an error.
When I use this code, I'm getting the graph with black dots:
s3d <- with(combined_data_2d, scatterplot3d(PC1, PC2, PC3, pch=20, cex.symbols = 3, angle = 65, col.grid="grey", y.margin.add=1.35, main="2D post SE"))
When I'm trying to use color codes for my grups, I keep getting an error:
s3d <- with(combined_data_2d, scatterplot3d(PC1, PC2, PC3, color = colors[as.data.frame(combined_data_2d$group)], pch=20, cex.symbols = 3, angle = 65, col.grid="grey", y.margin.add=1.35, main="2D post SE"))
I get an error:
Error in colors[as.data.frame(combined_data_2d$group)] : invalid subscript type 'list'
Any advice how to fix this?
I must add that this code used to work fine for me.