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Sequence index indices in ggplot2 using geom_tile ()

I am trying to use ggplot to create sequence graphs in order to maintain the same visual style in my article using sequence analysis. I AM:

library(ggplot2)
library(TraMineR)
library(dplyr)
library(tidyr)    
data(mvad)    
mvad_seq<-seqdef(mvad,15:length(mvad))
mvad_trate<-seqsubm(mvad_seq,method="TRATE")
mvad_dist<-seqdist(mvad_seq,method="OM",sm=mvad_trate)
cluster<-cutree(hclust(d=as.dist(mvad_dist),method="ward.D2"),k=6)
mvad$cluster<-cluster
mvad_long<-gather(select(mvad,id,contains("."),-matches("N.Eastern"),-matches("S.Eastern")),
                    key="Month",value="state",
                    Jul.93, Aug.93, Sep.93, Oct.93, Nov.93, Dec.93, Jan.94, Feb.94, Mar.94,
                    Apr.94, May.94, Jun.94, Jul.94, Aug.94, Sep.94, Oct.94, Nov.94, Dec.94, Jan.95,
                    Feb.95, Mar.95, Apr.95, May.95, Jun.95, Jul.95, Aug.95, Sep.95, Oct.95, Nov.95,
                    Dec.95, Jan.96, Feb.96, Mar.96, Apr.96, May.96, Jun.96, Jul.96, Aug.96, Sep.96,
                    Oct.96, Nov.96, Dec.96, Jan.97, Feb.97, Mar.97, Apr.97, May.97, Jun.97, Jul.97,
                    Aug.97, Sep.97, Oct.97, Nov.97, Dec.97, Jan.98, Feb.98, Mar.98, Apr.98, May.98,
                    Jun.98, Jul.98, Aug.98, Sep.98, Oct.98, Nov.98, Dec.98, Jan.99, Feb.99, Mar.99,
                    Apr.99, May.99, Jun.99)

mvad_long<-left_join(mvad_long,select(mvad,id,cluster))
ggplot(data=mvad_long,aes(x=Month,y=id,fill=state))+geom_tile()+facet_wrap(~cluster)

I am trying to build sequences on a cluster, and this gives me the following graph: Sequence index plot with ggplot

As you can see, there are spaces for identifiers that do not belong to the cluster represented by each face. I would like to get rid of these spaces so that the sequences appear on the stack in the same way as with the seqIplot () function TraMineR, as in the following figure: SeqIplot

Any suggestions on how to proceed?

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1 answer

Two small changes:

mvad_long$id <- as.factor(mvad_long$id)
ggplot(data=mvad_long,aes(x=Month,y=id,fill=state))+
       geom_tile()+facet_wrap(~cluster,scales = "free_y")

ggplot treated id as a numeric variable, not a factor, and then the scales were fixed.

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