Hi,
I hope I can explain my problem clearly....
I have a plink output file that I want to graph a heat map of the
PI_HAT estimates. I have the following code that I has worked in the
past but this time I'm getting the error:
In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else
paste0(labels, :
duplicated levels in factors are deprecated
My code:
require("ggplot2")
image = (p <- ggplot(db, aes(IID1, IID2)) +
geom_tile(aes(fill = PI_HAT), colour = "white") +
scale_fill_gradient2(low = "blue", high = "red") +
labs(x = "Individual 1",y = "Individual 2")
opts(axis.text.x = theme_text(angle=90)) +
opts(title="",legend.position = "right"))
I'm trying to figure out whether this is a problem with duplicated
PI-HAT estimates or duplicated ID pairings (though the latter
shouldn't be the case as I've used similar files in the past).
What else could be the problem?
P.S. My file is quite large (300K lines) so its pretty hard to
decipher the problem off the bat but the usual plink output file for
this type of file has the heading:
FID1 IID1 FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT