Using a for loop with ggplot2 to plot multiple graphs within a data frame - r

Question

Was just wondering if somebody could help with a problem I am having in R with a for loop using ggplot2. I have carried out some clustering to find patterns of data that change over time. There are various patterns in total with 38 graphs of patterns. The output of the clustering is to put side by side all 38 graphs which is nice for visualisation.
But I want to zoom in to individual graphs to zoom in to them for presentation and a cleared view of a pattern. This is easy manually, however, writing 38 versions of the same script but just with a different cluster in each one is very tedious, so I would like to create a for loop in order to achieve in one chunk of quick code. I have done this code (with some help online also), however, I am unable to get the ouput of the individual 38 graphs. the code itself works as I can specify one cluster which will then give me an output of that specific cluster, but I want to create a code that will creat all 38 different clusters.
The code I am using is as follows:
The data frame is called dfllgc, within which dfllgc$cluster contains information on the individual clusters. The for loop I am attempting is as follows but does not work. Any help would really really be appreciated!
for(cluster in dfllgc$cluster){
df<-subset(dataframAMIRllgc,cluster == 1:38)
df$Time_point<-factor(df.s$Time_point, levels = c("p3", "p15", "p30","p60"))
g<-ggplot(df, aes(x=Time_point, y=abundance, group=llgc, colour=llgc))+
geom_line(size=1.5)+
geom_point(size=4)+
ggtitle("Cluster 29: Patterns over time (5 genes) \n") +
xlab("\nAge") + ylab("Expression(CPM)\n")
print(g) }
Changing df<-subset(dataframAMIRllgc,cluster == 1:38) to == 1, or 15 etc, or any other cluster does indeed produce that one cluster, but not all 38 with 1:38.
Finally, with the title (ggtitle), is there a way to automate also the titles such that I can have a template, but that the cluster number as well as number of genes are automatically applied to the correct clusters?
Thank you so much! Any help would be much appreciated :)
example data
merge cluster Time_point llgc abundance
1 High[26-50%]p15 1 p15 High[26-50%] 166.5400335
38 High[26-50%]p3 1 p3 High[26-50%] 255.5007952
75 High[26-50%]p30 1 p30 High[26-50%] 122.1110473
112 High[26-50%]p60 1 p60 High[26-50%] 78.84340532
149 Low[0-10%]p15 1 p15 Low[0-10%] 86.40962037
186 Low[0-10%]p3 1 p3 Low[0-10%] 205.9750297
223 Low[0-10%]p30 1 p30 Low[0-10%] 60.23843127
260 Low[0-10%]p60 1 p60 Low[0-10%] 56.64259547
297 Medium[11-25%]p15 1 p15 Medium[11-25%] 165.2372227
334 Medium[11-25%]p3 1 p3 Medium[11-25%] 223.3891249
371 Medium[11-25%]p30 1 p30 Medium[11-25%] 155.1325448
408 Medium[11-25%]p60 1 p60 Medium[11-25%] 176.8285175
2 High[26-50%]p15 2 p15 High[26-50%] 85.21789981
39 High[26-50%]p3 2 p3 High[26-50%] 211.5359752
76 High[26-50%]p30 2 p30 High[26-50%] 35.7475454
113 High[26-50%]p60 2 p60 High[26-50%] 12.87995477
150 Low[0-10%]p15 2 p15 Low[0-10%] 77.20608808
187 Low[0-10%]p3 2 p3 Low[0-10%] 43.04550979
224 Low[0-10%]p30 2 p30 Low[0-10%] 34.88976766
261 Low[0-10%]p60 2 p60 Low[0-10%] 9.791146582
298 Medium[11-25%]p15 2 p15 Medium[11-25%] 46.21377697
335 Medium[11-25%]p3 2 p3 Medium[11-25%] 34.89603178
372 Medium[11-25%]p30 2 p30 Medium[11-25%] 14.18668175
409 Medium[11-25%]p60 2 p60 Medium[11-25%] 7.360330065
3 High[26-50%]p15 3 p15 High[26-50%] 47.75793997
40 High[26-50%]p3 3 p3 High[26-50%] 62.3529071
77 High[26-50%]p30 3 p30 High[26-50%] 17.8348889
114 High[26-50%]p60 3 p60 High[26-50%] 14.26366778
151 Low[0-10%]p15 3 p15 Low[0-10%] 138.1451371
188 Low[0-10%]p3 3 p3 Low[0-10%] 185.1184602
225 Low[0-10%]p30 3 p30 Low[0-10%] 63.52332626
262 Low[0-10%]p60 3 p60 Low[0-10%] 39.40566363
299 Medium[11-25%]p15 3 p15 Medium[11-25%] 26.32551336
336 Medium[11-25%]p3 3 p3 Medium[11-25%] 49.72067928
373 Medium[11-25%]p30 3 p30 Medium[11-25%] 8.288553629
410 Medium[11-25%]p60 3 p60 Medium[11-25%] 5.385031193

Answer 1

I'm not sure I 100% understand what you are trying to do but I think there is a problem with your subset and then you need to add a save function to the end. Hopefully this does what you want:
dfllgc$Time_point<-factor(dfllgc$Time_point, levels = c("p3", "p15", "p30","p60"))
for(cluster in unique(dfllgc$cluster)) {
g<-ggplot( dfllgc[ dfllgc$cluster == cluster, ],
aes(x=Time_point, y=abundance, group=llgc, colour=llgc)) +
geom_line(size=1.5) +
geom_point(size=4) +
ggtitle( paste0("Cluster ", cluster,": Patterns over time (5 genes)") ) +
xlab("Age") + ylab("Expression(CPM)")
ggsave(paste0("Cluster_", cluster,".png"), g)
}
Changes made:
removed the subset line and added the cluster subset/filter to ggplot line but it could just as easily be separate.
moved the factor conversion outside the for loop so it only needs to be applied once.
set the title and file name to change with each cluster