Plotting multiple graphs from multiple .csv files using R

Question

I'm quite new to R, and came across a problem I can't solve based on my knowledge/books/internet.

So here is the problem:

I've got 60 csv files, for which I want to plot a scatter plot each. They're all formatted the same, so I should (theoretically) be able to solve this task with a nice loop. Here is my code:

library(tools)
library(ggplot2)
files = dir('~/Klima_hist_CPL/tillnov/ClimDatK1/*.csv')
for (Y in list.files(path = "~/Klima_hist_CPL/tillnov/ClimDatK1/",pattern =".csv", 
     all.files = FALSE, full.names = TRUE, recursive = FALSE,
     ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)){
 myData<-read.csv(Y)
 pdf("~/Klima_hist_CPL/tillnov/ClimDatK1/mypdf.pdf", width = 4, height = 4)   
 print(ggplot(data = myData, aes(ACTION_DATE, TEMP)) 
   + geom_point(aes(x = myData$ACTION_DATE, y = myData$TEMP_SET),colour=('blue')) 
   + geom_point(aes(x = myData$ACTION_DATE, y = myData$TEMP_MEASURED), colour=('red') ))
#newFilename <-paste(file_path_sans_ext(basename(Y)),".jpg")
#fp <-paste('~/Klima_hist_CPL/tillnov/ClimDatK1/',newFilename)
#writeJPEG(output,file=fp,append=FALSE)
 dev.off()
}

As you can see I tried around a bit and used fragments of code from previous tasks. Unfortunately they don't work when combined.

Summing up:

Multiple CSV files
all formatted the same
each one should be plotted
I do not care if this results in one pdf or 60 of them

Paul Hiemstra · Accepted Answer · 2017-03-01 12:00:31Z

5

I would read all the data into one big data.frame and use facets to make all the plots in ggplot2. Some pseudo code which shows the general code pattern:

library(dplyr)
list_of_dfs = lapply(list.files('path/to/files', pattern = '*csv'), 
    function(x) {
        dat = read.csv(x)
        dat$fname = x
        return(dat)
    })
one_big_df = list_of_dfs %>% bind_rows()
one_big_df %>% ggplot(aes(x = x, y = y)) + geom_point() + facet_wrap(~ fname)

Saving the plot can then be done using ggsave;

ggsave('plot.png', width = 16, height = 9)

answered Mar 1, 2017 at 12:00

Paul Hiemstra

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2 Comments

Julius Over a year ago

Thank you very much! I tried your approach, but was hindered by some errors. But finally I managed to debug my own code and now it's working!

Paul Hiemstra Over a year ago

If you have specific questions, please feel free to ask more questions on SO.

Julius · Accepted Answer · 2017-03-01 15:45:46Z

0

Here is what worked for me ( just to lend a hand to somebody struggling with a similar problem)

The bottom line was to append full.names = T

to my files<-list.files(path = "~/Klima_hist_CPL/tillnov/ClimDatK1/", pattern = ".csv", full.names = T)

library(tools)
library(ggplot2)
files<-list.files(path = "~/Klima_hist_CPL/tillnov/ClimDatK1/", pattern = ".csv", full.names = T)
for (Y in files){
  myData<-read.csv(Y);
  fname <- basename(Y);
  fname <- substr(fname, 1, nchar(fname) - 4);
  pdf(
    sprintf("~/Klima_hist_CPL/tillnov/ClimDatK1/%s.pdf", fname), 
    width = 10, 
    height = 8
  );
  print(ggplot(data = myData, aes(ACTION_DATE, TEMP)) + 
      geom_point(aes(x = myData$ACTION_DATE, y = myData$TEMP_SET),colour=('blue')) + 
      geom_point(aes(x = myData$ACTION_DATE, y = myData$TEMP_MEASURED), colour=('red') ))
  dev.off() 
}

edited Mar 1, 2017 at 15:45

answered Mar 1, 2017 at 13:40

Julius

115 bronze badges

3 Comments

Paul Hiemstra Over a year ago

Could you explain what went wrong in the example in your question. Now we have to do this ourselves and guess what the exact fix is.

Julius Over a year ago

sure: I always got to this error message: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '1-2016.csv': No such file or directory by appending the full.names= T the file could be found and the loop worked

Paul Hiemstra Over a year ago

Aah, that is a classic error :), I have made that one a few times myself. Could you edit this information into the answer? Not everyone reads the comments.

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