[R] Reading a file with read.csv: two character rows not interpreted as I hope
hanson at depauw.edu
Wed Oct 31 14:50:00 CET 2007
OK, I fixed it myself! Here's the code. Of course, it mostly seems simple
once one gets it working... Thanks Jim. Bryan
sample.info = read.table(input.file.name, sep=",", as.is=TRUE, nrows=3) #
get the first three lines with sample info in character format
sample.names = sample.info[1,]
sample.colors = sample.info[2,]; sample.colors =
sample.class = sample.info[3,]; sample.class =
data = read.table(input.file.name, sep=",", skip=3)
colnames(data) = sample.names
On 10/30/07 10:53 PM, "Bryan Hanson" <hanson at depauw.edu> wrote:
> Jim, thanks for the suggestion. There is still something subtle
non-intuitive going on here. I adapted your code with minor changes
follows (I had to add the sep argument) but get different
c.names <- scan("file.csv", what='', nlines=1, sep=",") # read
> column names
c.options <- read.table("file.csv", as.is=TRUE, nrows=2, sep=",")
> # get
c.data <- read.table("file.csv", sep=",") # rest of the
colnames("file.csv") <- c.names
Your code works perfectly (you knew
> that!). My adaptation runs, but
c.options contains the first two lines, not
> lines 2 & 3, and c.data contains
the contents of the entire file as *factors*
> (data type of c.names &
c.options is correct - character). How strange!
> and this is an observation rather than a question: in your code, you
> and get the first line as characters, then you do read.table which
> 2 & 3 presumably because the first line, from read.table's
perspective is a
> hidden label (?), then the second time you use read.table
the hidden first
> line is ignored, as are the two lines with character data.
I really don't
> understand these behaviors, which is probably why I'm having
> the file!
On 10/30/07 8:40 PM, "jim holtman"
> <jholtman at gmail.com> wrote:
> Here is one way. You will probably use 'file'
> instead of textConnection
>> x.in <- textConnection('wavelength SampleA
> SampleB SampleC SampleD
> + color "green" "black" "black" "green"
> + class
> "Class 1" "Class 2" "Class 2" "Class 1"
> + 403 1.94E-01 2.14E-01 2.11E-01
> + 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
> + 415 1.70E-01
> 1.99E-01 1.94E-01 1.86E-01
> + 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
> 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
> + 432 1.42E-01 1.50E-01 1.62E-01
>> c.names <- scan(x.in, what='', nlines=1) # read column
> Read 5 items
>> c.options <- read.table(x.in, as.is=TRUE, nrows=2) #
> get lines 2-3
>> c.data <- read.table(x.in) # rest of the data
> colnames(c.data) <- c.names
>> c.options # here are lines
> V1 V2 V3 V4 V5
> 1 color green black
> black green
> 2 class Class 1 Class 2 Class 2 Class 1
>> c.data # your
> wavelength SampleA SampleB SampleC SampleD
> 1 403 0.194
> 0.214 0.211 0.183
> 2 409 0.192 0.189 0.200 0.182
> 415 0.170 0.199 0.194 0.186
> 4 420 0.159 0.191 0.216
> 5 426 0.150 0.166 0.172 0.158
> 6 432 0.142
> 0.150 0.162 0.148
> On 10/30/07, Bryan Hanson <hanson at depauw.edu>
>> Hi Folks... Œbeen playing with this for a while, with no luck, so
> I¹m hoping
>> someone knows it off the top of their head... Difficult to find
> this nuance
>> in the archives, as so many msgs deal with read.csv!
> trying to read a data file with the following structure (a little piece
> the actual data, they are actually csv just didn¹t paste with the
>> wavelength SampleA SampleB SampleC SampleD
>> color "green"
> "black" "black" "green"
>> class "Class 1" "Class 2" "Class 2" "Class 1"
> 403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
>> 409 1.92E-01 1.89E-01 2.00E-01
>> 415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
>> 420 1.59E-01 1.91E-01
> 2.16E-01 1.74E-01
>> 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
>> 432 1.42E-01
> 1.50E-01 1.62E-01 1.48E-01
>> Columns after the first one are sample
> names. 2nd row is the list of colors
>> to use in later plotting. 3rd row is
> the class for later manova. The rest
>> of it is x data in the first column
> with y1, y2...following for plotting.
>> I can read the file w/o the color
> or class rows with read.csv just fine,
>> makes a nice data frame with proper
> data types. The problem comes when
>> parsing the 2nd and 3rd rows. Here¹s
> the code:
>> data = read.csv("filename", header=TRUE) # read in data
> color = data[1,]; color = data[-1] # capture color info & throw out 1st
>> class = data[2,]; class = class[-1] # capture category info & throw
> out 1st
>> cleaned.data = data[-1,] # remove color & category
> info for matrix
>> cleaned.data = data[-1,]
>> freq = data[,1] #
> capture frequency info
>> What happens is that freq is parsed as factors,
> and the color and class are
>> parsed as a data frames of factors.
>> I need
> color and class to be characters which I can pass to functions in the
> typical way one uses colors and levels.
>> I need the freq & the cleaned.data
> info as numeric for plotting.
>> I don¹t feel I¹m far off from things
> working, but that¹s where you all come
>> in! Seems like an argument of
> as.something is needed, but the ones I¹ve
>> tried don¹t work. Would it help
> to put color and class above the x,y data
>> in the file, then clean it
>> Btw, I¹m on a Mac using R 2.6.0.
>> Thanks in advance,
>> Bryan Hanson
>> Professor of Chemistry &
>> [[alternative HTML version deleted]]
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