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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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multiple linetypes for ellipses based on treatment #810

Open iferuzan opened 7 years ago

iferuzan commented 7 years ago

Hi,

I am trying to change the line types for the ellipses based on my Treatments. Here are the commands I am using:

PCG.ord <- ordinate(PCG, "PCoA") p1 = plot_ordination(PCG, PCG.ord, type="samples", shape="Treatment", title="PCG") p1 + geom_point(size=2) + ggtitle("PCG") + theme(plot.title = element_text(hjust = 0.5)) + xlab("PC1") + ylab("PC2")+ scale_shape_discrete(breaks=c("Initial Time","10 Weeks Control","10 Weeks Treatment")) + stat_ellipse(type="norm")

Again, my problem is that I am trying to have different ellipse linetypes for my three Treatments (Initial Time, 10 Weeks Control, and 10 Weeks Treatment). Is there a way to do this? I tried using scale_linetype_manual but could not get it to work...

Any help is much appreciated!

kthrnmcbride commented 6 years ago

I know this question was asked over a year ago, but I was having a similar issue so I'll put the solution in case anyone in the future needs it.

pcoaord + stat_ellipse(aes(lty=factor(location)), type = "t", level = 0.95) + scale_linetype_manual(values=c(1,2)) + theme_bw()

for your code I would put: lty=factor(Treatment)) and follow it with scale_linetype_manual(values=c(1,2,3) or whatever you would want the line types to be.