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I'm trying to read data into R from a text file such that I can plot it:

coupling <- read.table("~/table.format",stringsAsFactors = FALSE, sep='\t')

A row from this table looks as follows:

133 0.0116, 0.0226, 0.0236, 0.0244, 0.0264, 0.0124, 0.013, 0.014, 0.0158, 0.034, 0.0348, 0.0356, 0.0372  329777.0, -236464.0, -348470.0, -554708.0, -471896.0, 538782.0, 695291.0, 812729.0, 983141.0, 208212.0, 214012.0, 366636.0, 343232.0

Where the columns (residue, delay, height) are separated by tabs and data within the columns is separated by ','. I would now like to plot height vs delay, so I attempt to assign the columns to variables:

 xdata <- c(coupling[1,2])
 ydata <- c(coupling[1,3])

However, if I try and plot plot(xdata,ydata) I get the following errors:

Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
5: In min(x) : no non-missing arguments to min; returning Inf
6: In max(x) : no non-missing arguments to max; returning -Inf

Printing xdata (and ydata) gives a variable of the form:

xdata
[1] "0.0116, 0.0226, 0.0236, 0.0244, 0.0264, 0.0124, 0.013, 0.014, 0.0158, 0.034, 0.0348, 0.0356, 0.0372 "

Presumably R can't plot this with the quotes in place. I've tried a few alternatives to try and get round this, however, none of these have worked:

newxdata <-as.numeric(xdata)

Returns error:

    Warning message:
    NAs introduced by coercion

Print gets me close:

print(xdata,quote=FALSE)

This seems to do the trick; the output loses the quotes:

[1] 0.0116, 0.0226, 0.0236, 0.0244, 0.0264, 0.0124, 0.013, 0.014, 0.0158, 0.034, 0.0348, 0.0356, 0.0372

But if I assign it to a variable, the quotes reappear and I still can't plot the data:

newxdata <- c(print(xdata,quote=FALSE))
 newxdata
[1] "0.0116, 0.0226, 0.0236, 0.0244, 0.0264, 0.0124, 0.013, 0.014, 0.0158, 0.034, 0.0348, 0.0356, 0.0372 "

How can I get around this problem?

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2 Answers2

3

You need some modifications first and then it will work. The reason for the quotes is that you have a character vector of length 1 that you need to convert into a numerical vector of length 13:

#initial data set: character vector of length 1
a <- "0.0116, 0.0226, 0.0236, 0.0244, 0.0264, 0.0124, 0.013, 0.014, 0.0158, 0.034, 0.0348, 0.0356, 0.0372 "

#function to trim leading and trailing spaces **see bottom of answer
trim <- function (x) gsub("^\\s+|\\s+$", "", x)

#first use strsplit to split the long string into separate string elements
#that are comma separated.
#Then use trim on each element to remove leading and trailing spaces
b <- trim(strsplit(a, ',')[[1]])

#finally use as.numeric to convert to numbers
c <- as.numeric(b)

Variable c can now be used in plot

Output:

> c
 [1] 0.0116 0.0226 0.0236 0.0244 0.0264 0.0124 0.0130 0.0140 0.0158 0.0340 0.0348 0.0356 0.0372

Function trim was taken from here

EDIT

Apparently as per @zero323 's comment you don't even need to trim the character vector. So, this works fine in one call:

> as.numeric(strsplit(a, ',')[[1]])
 [1] 0.0116 0.0226 0.0236 0.0244 0.0264 0.0124 0.0130 0.0140 0.0158 0.0340 0.0348 0.0356 0.0372
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LyzandeR
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2

You may also use scan (data from @LyzandeR's post)

 scan(text=a, what=numeric(), sep=",", quiet=TRUE)
 #[1] 0.0116 0.0226 0.0236 0.0244 0.0264 0.0124 0.0130 0.0140 0.0158 0.0340
 #[11] 0.0348 0.0356 0.0372

You could directly use scan to read it from the file with sep=","

 scan("~/table.format", what=numeric(), sep=",", quiet=TRUE) #not tested
akrun
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