I'm creating a barplot using ggplot2, and when I change the colour palette using scale_fill_manual, it is putting borders around the colour fill, so some of the values, particularly the smaller percentages, are difficult to see or completely obscured.
I'm plotting % of samples made up of different fungal phyla. The data is from a phyloseq object, where I summed the relative abundance of different phyla then transformed to a dataframe as I have more experience working with df objects in ggplot2. Example of how the data is organised: Sample Data
The code I'm using to make the boxplot:
scat.melt%>%
ggplot()+
geom_bar(aes(y=Abundance, x=Sample, color=Phylum, fill=Phylum), stat="identity", position="stack")+
facet_wrap(~ReleaseTime, scales="free")+
theme(panel.background = element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank(), strip.background = element_rect(fill="white"))+
ylab("Relative Abundance (%)\n")+
scale_fill_manual(values=colorBlindGrey8)
It is exactly what I want except for the lines- I was thinking that it is because in the data rows the phyla are broken up into their OTU's, so they are still being represented as discrete groups in the barplot although they are the same phyla so still represented as the same colour. However when I remove the scale_fill_manual argument, and use the default colour palette, I don't have this issue (there are no borders around the colours).
I also thought applying a group_by argument to the dataframe before plotting would potentially help, so tried that:
scat.melt<-scat.melt %>%
group_by(pick(ReleaseTime, Phylum, Sample))
To no avail.