Plot data in multiple files using ggplot

Question

I have a time series data file which has the concentration of 4 metabolites A, B, AE and E over time. I have many data files of this type (around 100). I want to plot the time series for all the four metabolites in all the files in one graph. Each metabolite is assigned a specifc color.

I compiled the below code, however it plots data in only one file (the last one). I think that is because when ever I call ggplot() it creates a new plot. I've tried creating the plot outside of the four loop and it didn't work.

p = NULL

for(i in 1:length(filesToProcess)){
  fileName = filesToProcess[i]

  fileContent = read.csv(fileName)
  #fileContent$Time <- NULL

    p <- ggplot()+ 
    geom_line(data = fileContent, aes(x = Time, y = A, color = "A"), size =0.8) +
    geom_line(data = fileContent, aes(x = Time, y = B, color = "B"), size =0.8)  +
    geom_line(data = fileContent, aes(x = Time, y = AE, color = "AE"), size =0.8)  +
    geom_line(data = fileContent, aes(x = Time, y = E, color = "E"), size =0.8)  +
    xlab('Time') +
    ylab('Metabolite Concentration')+
    ggtitle('Step Scan') +
    labs(color="Metabolites")

}
plot(p)

Below is the graph

Sample files can be found here

baptiste · Accepted Answer · 2016-07-31 12:01:15Z

3

I usually take the following approach (untested, for lack of a reproducible example)

read_one <- function(f, ...){
  w <- read.csv(f, ...)
  m <- reshape2::melt(w, id = c("Time"))
  m$source <- tools::file_path_sans_ext(f) # keep track of filename
  m
}

plot_one <- function(d){
  ggplot(d, aes(x=Time, y=value)) + 
    geom_line(aes(colour=variable), size = 0.8) +
    ggtitle('Step Scan') +
    labs(x = 'Time', y = 'Metabolite Concentration', color="Metabolites")
}

## strategy 1 (multiple independent plots)

ml <- lapply(filesToProcess, read_one)
pl <- lapply(ml, plot_one)

gridExtra::grid.arrange(grobs = pl)

## strategy 2: facetting

m <- plyr::ldply(filesToProcess, read_one)
ggplot(m, aes(x=Time, y=value)) + 
  facet_wrap(~source) +
  geom_line(aes(colour=variable), size = 0.8) +
  ggtitle('Step Scan') +
  labs(x = 'Time', y = 'Metabolite Concentration', color="Metabolites")

answered Jul 31, 2016 at 12:01

baptiste

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1 Comment

SriniShine Over a year ago

thank you for the answer. I'm trying to wrap my head around your solution. It looks bit complicated for me. Also I've included few sample files.

Philippe Marchand · Accepted Answer · 2016-07-31 16:56:37Z

0

~~Since plot(p) is outside the loop, it will only plot the last graph produced. Move plot(p) inside the loop.~~

~~Note: While the question is somewhat ambiguous, I'm assuming you want one graph per input file.~~

EDIT: To put all data in a single plot, assuming all your files have same columns in same order.

all_data <- lapply(filesToProcess, read.csv)
fileContent <- do.call(rbind, all_data)

Then you can run the ggplot code exactly as you did above (without a loop).

edited Jul 31, 2016 at 16:56

answered Jul 31, 2016 at 14:06

Philippe Marchand

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2 Comments

SriniShine Over a year ago

@Marchand I need one graph for data in all the files.

SriniShine Over a year ago

@Marchand thank you for the suggestion. Yes all the files have the same columns in the same order (Time, A, A|E, B, E). HOwere I tried your method and the plot doesn't look what it should look like. Also I've included few sample files.

SriniShine · Accepted Answer · 2016-08-01 11:05:31Z

I think I solved the problem. The answer is bit crude I admit. However if I could initialize the "p" variable outside the for loop it solves the problem.

filesToProcess = readLines("FilesToProcess.txt")

#initializing the variable with ggplot() object
p <- ggplot()

for(i in 1:length(filesToProcess)){
  fileName = filesToProcess[i]
  fileContent = read.csv(fileName)

  p <- p + 
  geom_line(data = fileContent, aes(x = Time, y = A, color = "A"), size =0.8) +
  geom_line(data = fileContent, aes(x = Time, y = B, color = "B"), size =0.8)  +
  geom_line(data = fileContent, aes(x = Time, y = AE, color = "AE"), size =0.8)  +
  geom_line(data = fileContent, aes(x = Time, y = E, color = "E"), size =0.8)

}

p <- p + theme_bw() + scale_x_continuous(breaks=1:20) + 
  xlab('Time') +
  ylab('Metabolite Concentration')+
  ggtitle('Step Scan') +
  labs(color="Legend text")
plot(p)

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