I've been trying to recreate this post on a combination of stacked bar/area plot. I have some problems with missing values though.
Here's my data: https://www.dropbox.com/sh/pnkspwnn1qslm6u/JapTKCwqMS
What I run is;
wa=read.table('wa_class.txt', sep="", header=F, na.string="0")
names(wa)=c("Class","Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec")
wam=melt(wa)
wam$variablen=as.numeric(wam$variable)
How it looks like
> head(wam)
Class variable value variablen
1 Actinobacteria Jan 38.115163 1
2 Flavobacteria Jan NA 1
3 Sphingobacteria Jan 3.640469 1
4 Alphaproteobacteria Jan 13.631663 1
5 Betaproteobacteria_b28 Jan 3.718671 1
6 Betaproteobacteria Jan 14.732354 1
ggplot(na.omit(wam[,c("Class","value","variablen")]), aes(wam,x=variablen, y=value, fill=Class)) + geom_area(color="black") + geom_linerange(aes(ymax=value), position="stack") + scale_x_continuous(breaks=1:max(wam$variablen)) + labs(title="Water", x="Month", y="Relative abundance (%)")
...so I have tried to correct for the missing values with use na.omit on the variables I plot. However, I get layers in the plot which e.g. is overriding each other (see dropbox folder).
I found this post (see dropbox folder) which corrected for it, but seemed only to have one. And I couldn't reproduce it since the link to the data is dead.
Any help would really be appreciated!
Thanks,
Jo
One solution is to read zeros as zero values. If you don't use
na.string="0"
, the plot will look like this: