So I have a text file that looks like this: "Label" "X" "Y" "Slice" 1 "Field_1_R3D_D3D_PRJ_w617.tif" 348 506 1 2 "Field_1_R3D_D3D_PRJ_w617.tif" 359 505 1 3 "Field_1_R3D_D3D_PRJ_w617.tif" 356 524 1 4 "Field_1_R3D_D3D_PRJ_w617.tif" 2 0 1 5 "Field_1_R3D_D3D_PRJ_w617.tif" 412 872 1 6 "Field_1_R3D_D3D_PRJ_w617.tif" 422 863 1 7 "Field_1_R3D_D3D_PRJ_w617.tif" 429 858 1 8 "Field_1_R3D_D3D_PRJ_w617.tif" 429 880 1 9 "Field_1_R3D_D3D_PRJ_w617.tif" 437 865 1 10 "Field_1_R3D_D3D_PRJ_w617.tif" 447 855 1 11 "Field_1_R3D_D3D_PRJ_w617.tif" 450 868 1 12 "Field_1_R3D_D3D_PRJ_w617.tif" 447 875 1 13 "Field_1_R3D_D3D_PRJ_w617.tif" 439 885 1 14 "Field_1_R3D_D3D_PRJ_w617.tif" 2 8 1 What it represents are the locations of centromeres per nucleus in a microscope image. What I need to do is do a dist() on each grouping (the grouping being separated by the low values of x and y's) and then compute an average. The part that I'm having trouble with is writing code that will allow R to separate these objects. Do I have to find some way of creating separate data frames for each object? Or is there a way to parse the file and generate a single data frame of all the pairwise distances? Any suggestions or example code would be much appreciated. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Doing-dist-on-separate-objects-in-a-text-file-tp3994515p3994515.html Sent from the R help mailing list archive at Nabble.com.
Doing dist on separate objects in a text file
5 messages · R. Michael Weylandt, David Winsemius, ScottDaniel +1 more
Perhaps split() directly or more abstractly tapply() from base or one of the d_ply() from plyr? Michael
On Sat, Nov 5, 2011 at 7:20 PM, ScottDaniel <scottdaniel25 at gmail.com> wrote:
So I have a text file that looks like this: ? ? ? ?"Label" "X" ? ? "Y" ? ? "Slice" 1 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?348 ? ? 506 ? ? 1 2 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?359 ? ? 505 ? ? 1 3 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?356 ? ? 524 ? ? 1 4 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?2 ? ? ? 0 ? ? ? 1 5 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?412 ? ? 872 ? ? 1 6 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?422 ? ? 863 ? ? 1 7 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?429 ? ? 858 ? ? 1 8 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?429 ? ? 880 ? ? 1 9 ? ? ? "Field_1_R3D_D3D_PRJ_w617.tif" ?437 ? ? 865 ? ? 1 10 ? ? ?"Field_1_R3D_D3D_PRJ_w617.tif" ?447 ? ? 855 ? ? 1 11 ? ? ?"Field_1_R3D_D3D_PRJ_w617.tif" ?450 ? ? 868 ? ? 1 12 ? ? ?"Field_1_R3D_D3D_PRJ_w617.tif" ?447 ? ? 875 ? ? 1 13 ? ? ?"Field_1_R3D_D3D_PRJ_w617.tif" ?439 ? ? 885 ? ? 1 14 ? ? ?"Field_1_R3D_D3D_PRJ_w617.tif" ?2 ? ? ? 8 ? ? ? 1 What it represents are the locations of centromeres per nucleus in a microscope image. What I need to do is do a dist() on each grouping (the grouping being separated by the low values of x and y's) and then compute an average. The part that I'm having trouble with is writing code that will allow R to separate these objects. Do I have to find some way of creating separate data frames for each object? Or is there a way to parse the file and generate a single data frame of all the pairwise distances? Any suggestions or example code would be much appreciated. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Doing-dist-on-separate-objects-in-a-text-file-tp3994515p3994515.html Sent from the R help mailing list archive at Nabble.com.
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
On Nov 5, 2011, at 7:20 PM, ScottDaniel wrote:
So I have a text file that looks like this: "Label" "X" "Y" "Slice" 1 "Field_1_R3D_D3D_PRJ_w617.tif" 348 506 1 2 "Field_1_R3D_D3D_PRJ_w617.tif" 359 505 1 3 "Field_1_R3D_D3D_PRJ_w617.tif" 356 524 1 4 "Field_1_R3D_D3D_PRJ_w617.tif" 2 0 1 5 "Field_1_R3D_D3D_PRJ_w617.tif" 412 872 1 6 "Field_1_R3D_D3D_PRJ_w617.tif" 422 863 1 7 "Field_1_R3D_D3D_PRJ_w617.tif" 429 858 1 8 "Field_1_R3D_D3D_PRJ_w617.tif" 429 880 1 9 "Field_1_R3D_D3D_PRJ_w617.tif" 437 865 1 10 "Field_1_R3D_D3D_PRJ_w617.tif" 447 855 1 11 "Field_1_R3D_D3D_PRJ_w617.tif" 450 868 1 12 "Field_1_R3D_D3D_PRJ_w617.tif" 447 875 1 13 "Field_1_R3D_D3D_PRJ_w617.tif" 439 885 1 14 "Field_1_R3D_D3D_PRJ_w617.tif" 2 8 1 What it represents are the locations of centromeres per nucleus in a microscope image. What I need to do is do a dist() on each grouping (the grouping being separated by the low values of x and y's) and then compute an average. The part that I'm having trouble with is writing code that will allow R to separate these objects.
I'm having trouble figuring out what you mean by "separating the objects". Each row is a separate reading, and I think you just want pairwise distances, right?
Do I have to find some way of creating separate data frames for each object?
I don't think so. You need to read this file into a data.frame which should be fairly trivial with read.table is you specify the header=TRUE parameter.
Or is there a way to parse the file and generate a single data frame of all the pairwise distances?
Then assuming there is now a data.frame named "dat" with those values:
dist( cbind(dat$X, dat$Y))
One stumbling block might have been recognizing that the dist function
will not work with two x and y arguments but rather requires a matrix
(or something coercible to a matrix) as its first argument. This
would also have worked:
dist(dat[ , c("X", "Y")])
David. > Any > suggestions or example code would be much appreciated. Thanks! > > -- > View this message in context: http://r.789695.n4.nabble.com/Doing-dist-on-separate-objects-in-a-text-file-tp3994515p3994515.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT
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Is this what you want:
x <- read.table(textConnection('"Label" "X" "Y" "Slice"
+ 1 "Field_1_R3D_D3D_PRJ_w617.tif" 348 506 1 + 2 "Field_1_R3D_D3D_PRJ_w617.tif" 359 505 1 + 3 "Field_1_R3D_D3D_PRJ_w617.tif" 356 524 1 + 4 "Field_1_R3D_D3D_PRJ_w617.tif" 2 0 1 + 5 "Field_1_R3D_D3D_PRJ_w617.tif" 412 872 1 + 6 "Field_1_R3D_D3D_PRJ_w617.tif" 422 863 1 + 7 "Field_1_R3D_D3D_PRJ_w617.tif" 429 858 1 + 8 "Field_1_R3D_D3D_PRJ_w617.tif" 429 880 1 + 9 "Field_1_R3D_D3D_PRJ_w617.tif" 437 865 1 + 10 "Field_1_R3D_D3D_PRJ_w617.tif" 447 855 1 + 11 "Field_1_R3D_D3D_PRJ_w617.tif" 450 868 1 + 12 "Field_1_R3D_D3D_PRJ_w617.tif" 447 875 1 + 13 "Field_1_R3D_D3D_PRJ_w617.tif" 439 885 1 + 14 "Field_1_R3D_D3D_PRJ_w617.tif" 2 8 1'), header = TRUE, as.is = TRUE)
closeAllConnections()
# create column to segment the data
x$mark <- cumsum(x$X < 10)
# now remove separators
x <- subset(x, X >= 10)
# now split the data
x.s <- split(x, x$mark)
# now do the dist
lapply(x.s, function(a) dist(a[, c("X", "Y")]))
$`0`
1 2
2 11.04536
3 19.69772 19.23538
$`1`
5 6 7 8 9 10
11 12
6 13.453624
7 22.022716 8.602325
8 18.788294 18.384776 22.000000
9 25.961510 15.132746 10.630146 17.000000
10 38.910153 26.248809 18.248288 30.805844 14.142136
11 38.209946 28.442925 23.259407 24.186773 13.341664 13.341664
12 35.128336 27.730849 24.758837 18.681542 14.142136 20.000000
7.615773
13 29.966648 27.802878 28.792360 11.180340 20.099751 31.048349
20.248457 12.806248
On Sun, Nov 6, 2011 at 3:49 PM, ScottDaniel <scottdaniel25 at gmail.com> wrote:
On Nov 5, 2011, at 7:20 PM, ScottDaniel wrote:
So I have a text file that looks like this: "Label" ? ? "X" ? ? "Y" ? ? "Slice" 1 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?348 ? ? 506 ? ? 1 2 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?359 ? ? 505 ? ? 1 3 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?356 ? ? 524 ? ? 1 4 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?2 ? ? ? 0 ? ? ? 1 5 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?412 ? ? 872 ? ? 1 6 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?422 ? ? 863 ? ? 1 7 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?429 ? ? 858 ? ? 1 8 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?429 ? ? 880 ? ? 1 9 ? "Field_1_R3D_D3D_PRJ_w617.tif" ?437 ? ? 865 ? ? 1 10 ?"Field_1_R3D_D3D_PRJ_w617.tif" ?447 ? ? 855 ? ? 1 11 ?"Field_1_R3D_D3D_PRJ_w617.tif" ?450 ? ? 868 ? ? 1 12 ?"Field_1_R3D_D3D_PRJ_w617.tif" ?447 ? ? 875 ? ? 1 13 ?"Field_1_R3D_D3D_PRJ_w617.tif" ?439 ? ? 885 ? ? 1 14 ?"Field_1_R3D_D3D_PRJ_w617.tif" ?2 ? ? ? 8 ? ? ? 1 What it represents are the locations of centromeres per nucleus in a microscope image. What I need to do is do a dist() on each grouping (the grouping being separated by the low values of x and y's) and then compute an average. The part that I'm having trouble with is writing code that will allow R to separate these objects.
I'm having trouble figuring out what you mean by "separating the objects". Each row is a separate reading, and I think you just want pairwise distances, right?
What I mean is that rows 1-3 represent one group of centromeres and rows 5-13 represent a second group. So I want to do a separate dist on each group (i.e. I want a pair wise distance for rows 1 and 3 but not 1 and 12). Does that clear thing up? -- View this message in context: http://r.789695.n4.nabble.com/Doing-dist-on-separate-objects-in-a-text-file-tp3994515p3996701.html Sent from the R help mailing list archive at Nabble.com. ? ? ? ?[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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