Hello,

I am following the DeSeq2 tutorial in Phyloseq and I'm using the following code to plots OTUs by Genus, coloured by Order. I am doing multiple plots, which I want to then group together and the problem is that because some have different Orders included there is no colour consensus over the plots, for example so all Bacteroidales points are always red . Im struggling to find an answer to this? 

library("ggplot2")

theme_set(theme_bw())

scale_fill_discrete <- function(palname = "Set1", ...) {

scale_fill_brewer(palette = palname, ...)

}

# Order order

x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))

x = sort(x, TRUE)

sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))

# Genus order

x = tapply(sigtab$log2FoldChange, sigtab$Genus, function(x) max(x))

x = sort(x, TRUE)

sigtab$Genus = factor(as.character(sigtab$Genus), levels=names(x))

ggplot(sigtab, aes(x=Genus, y=log2FoldChange, color=Order)) + geom_point(size=6) +

theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5))

Dot_plot_UN_LS1 <- ggplot(sigtab, aes(x=Genus, y=log2FoldChange, color=Order)) + geom_point(size=6) + theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5))

Dot_plot_UN_LS1 + ggtitle("Differentially abundant OTUs (uninfected vs LS 1)") + theme(plot.title = element_text(size = 10, face = "bold"))

Any help appreciated,

Cheers,

Sarah