1
$\begingroup$

I have a collection of bacteria data from approximately 140 monitoring locations in California. I would like to produce a scatterplot for each monitoring location with the Sampling Date on the Y-axis and the Bacteria Data on the X-axis. The Sampling Date, Bacteria Data, and Monitoring Location all reside within their own column.

I've come up with the below code:

## Create List of Files ##
filenames <- list.files(path = "C:\\Users\\...")

## Combine into one CSV ##
All_Data <- ldply(filenames, read.csv)
All_Data$SampleDate <- as.Date(All_Data$SampleDate, origin="1899-12-30")

## Save CSV for possible future use ##
write.csv(All_Data, file= "C://Users//...", row.names = FALSE)


## Construct Plots ##
ggplot(All_Data) + geom_point(mapping =aes(SampleDate, Total.Result)) + facet_wrap( ~ Identifier) +ylim(0,20000)

but this produces the below plot where every single location is crammed into the plot frame. Is there a way to print each plot individually to a folder? enter image description here

I tried to incorporate the subset function like so

ggplot(All_Data) + geom_point(mapping =aes(SampleDate, Total.Result)) + facet_wrap( ~ subset(All_Data, Identifier)) +ylim(0,20000)

but received the error

Error in subset.data.frame(All_Data, Identifier) : 
  'subset' must be logical

Alternatively, is it better to do this through some sort of loop through the original 15 csvs that I've combined together? I would still have the challenge of creating one plot per monitoring location. Thanks in advance for any suggestions!

$\endgroup$
  • $\begingroup$ Just loop trough your monitoring location. $\endgroup$ – lcrmorin Jan 9 at 22:56
  • $\begingroup$ @lcrmorin Could you explain what you mean by this? I'm still very new to R and haven't had much luck constructing loops on my own. $\endgroup$ – Water_Programs Jan 9 at 23:06
3
$\begingroup$

something like this might work:

library(plyr)

# initialize All_Data around here

dlply(All_Data, 'Identifier', function(dataSubset) {
  g <- ggplot(dataSubset) + geom_point(mapping =aes(SampleDate, Total.Result)) + ylim(0,20000)
  file_name <- paste0("Scatter_", unique(dataSubset$Identifier), ".tiff", sep="")
  ggsave(file_name,g)
})

(I didn't test it)

| improve this answer | |
$\endgroup$
  • $\begingroup$ Ah! This is great! Yours works much faster than what I was using below AND solves some errors that popped up in a few of my plots. Thanks! $\endgroup$ – Water_Programs Jan 10 at 20:33
1
$\begingroup$

I finally figured out something that works:

plot_list = list()
for (i in Monitoring_Locations){
     p = ggplot(All_Data) +geom_point(aes(SampleDate, Total.Result))
     plot_list[[i]] = p
             }
for (i in Monitoring_Locations) {
  file_name = paste("Scatter", i, ".tiff", sep="")
  tiff(file_name)
  print(plot_list[[i]])
  dev.off()
}

The only problem is, this prints out an identical plot for each separate location, essentially fitting ALL of the data in column Total.Result onto one plot and replicating it 164 times. Is there something missing in my loop that would tell it to group the data based off of the Identifier?

| improve this answer | |
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.