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Christos Hatzis

2007-Feb-01 20:05 UTC

[R] Lining up x-y datasets based on values of x

Hi,

I was wondering if there is a direct approach for lining up 2-column
matrices according to the values of the first column.  An example and a
brute-force approach is given below:

x <- cbind(1:10, runif(10))
y <- cbind(5:14, runif(10))
z <- cbind((-4):5, runif(10))

xx <- seq( min(c(x[,1],y[,1],z[,1])), max(c(x[,1],y[,1],z[,1])), 1)
w <- cbind(xx, matrix(rep(0, 3*length(xx)), ncol=3)) 

w[ xx >= x[1,1] & xx <= x[10,1], 2 ] <- x[,2]
w[ xx >= y[1,1] & xx <= y[10,1], 3 ] <- y[,2]
w[ xx >= z[1,1] & xx <= z[10,1], 4 ] <- z[,2]

w 

I appreciate any pointers.

Thanks.
 
Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite 5350
Woburn, MA 01801
Tel: 781-938-3830
www.nuverabio.com

Marc Schwartz

2007-Feb-01 20:28 UTC

head link

[R] Lining up x-y datasets based on values of x

On Thu, 2007-02-01 at 15:05 -0500, Christos Hatzis
wrote:> Hi,
> 
> I was wondering if there is a direct approach for lining up 2-column
> matrices according to the values of the first column.  An example and a
> brute-force approach is given below:
> 
> x <- cbind(1:10, runif(10))
> y <- cbind(5:14, runif(10))
> z <- cbind((-4):5, runif(10))
> 
> xx <- seq( min(c(x[,1],y[,1],z[,1])), max(c(x[,1],y[,1],z[,1])), 1)
> w <- cbind(xx, matrix(rep(0, 3*length(xx)), ncol=3)) 
> 
> w[ xx >= x[1,1] & xx <= x[10,1], 2 ] <- x[,2]
> w[ xx >= y[1,1] & xx <= y[10,1], 3 ] <- y[,2]
> w[ xx >= z[1,1] & xx <= z[10,1], 4 ] <- z[,2]
> 
> w 
> 
> I appreciate any pointers.
> 
> Thanks.
How about this:

x <- cbind(1:10, runif(10))
y <- cbind(5:14, runif(10))
z <- cbind((-4):5, runif(10))

colnames(x) <- c("X", "Y")
colnames(y) <- c("X", "Y")
colnames(z) <- c("X", "Y")

xy <- merge(x, y, by = "X", all = TRUE)
xyz <- merge(xy, z, by = "X", all = TRUE)

xyz[is.na(xyz)] <- 0
> xyz    X       Y.x       Y.y         Y
1  -4 0.0000000 0.0000000 0.3969099
2  -3 0.0000000 0.0000000 0.8943127
3  -2 0.0000000 0.0000000 0.4882819
4  -1 0.0000000 0.0000000 0.0275787
5   0 0.0000000 0.0000000 0.7562341
6   1 0.6873130 0.0000000 0.6185218
7   2 0.1930880 0.0000000 0.2318025
8   3 0.1164783 0.0000000 0.7336057
9   4 0.7408532 0.0000000 0.3006347
10  5 0.7112887 0.6383823 0.8515126
11  6 0.2719079 0.5952721 0.0000000
12  7 0.2067017 0.8178048 0.0000000
13  8 0.2085043 0.5714917 0.0000000
14  9 0.2251435 0.4032660 0.0000000
15 10 0.3471888 0.5247478 0.0000000
16 11 0.0000000 0.6899197 0.0000000
17 12 0.0000000 0.7188912 0.0000000
18 13 0.0000000 0.9133252 0.0000000
19 14 0.0000000 0.9186001 0.0000000

Note that 'xyz' will be a data frame, so just use as.matrix(xyz) to
coerce back to a numeric matrix if needed.

See ?merge

HTH,

Marc Schwartz

Gabor Grothendieck

2007-Feb-02 00:24 UTC

head link

[R] Lining up x-y datasets based on values of x

The zoo package has a multiway merge with optional zero fill.
Here are two ways:

library(zoo)
merge(x = zoo(x[,2], x[,1]),
      y = zoo(y[,2], y[,1]),
      z = zoo(z[,2], z[,1]),
      fill = 0)

# or

library(zoo)
X <- list(x = x, y = y, z = z)
merge0 <- function(..., fill = 0) merge(..., fill = fill)
do.call("merge0", lapply(X, function(x) zoo(x[,2], x[,1])))

To get more info on zoo try:

vignette("zoo")

On 2/1/07, Christos Hatzis <christos at nuverabio.com>
wrote:> Hi,
>
> I was wondering if there is a direct approach for lining up 2-column
> matrices according to the values of the first column.  An example and a
> brute-force approach is given below:
>
> x <- cbind(1:10, runif(10))
> y <- cbind(5:14, runif(10))
> z <- cbind((-4):5, runif(10))
>
> xx <- seq( min(c(x[,1],y[,1],z[,1])), max(c(x[,1],y[,1],z[,1])), 1)
> w <- cbind(xx, matrix(rep(0, 3*length(xx)), ncol=3))
>
> w[ xx >= x[1,1] & xx <= x[10,1], 2 ] <- x[,2]
> w[ xx >= y[1,1] & xx <= y[10,1], 3 ] <- y[,2]
> w[ xx >= z[1,1] & xx <= z[10,1], 4 ] <- z[,2]
>
> w
>
> I appreciate any pointers.
>
> Thanks.
>
> Christos Hatzis, Ph.D.
> Nuvera Biosciences, Inc.
> 400 West Cummings Park
> Suite 5350
> Woburn, MA 01801
> Tel: 781-938-3830
> www.nuverabio.com
>
> ______________________________________________
> R-help at stat.math.ethz.ch 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.
>

Christos Hatzis

2007-Feb-02 04:01 UTC

head link

[R] Lining up x-y datasets based on values of x

Thanks Gabor.

This is along the lines of what I was looking for.  In fact the merge
function for zoo objects (ordered) turns out to be almost an order of
magnitude faster than the generic merge function for my problem:
> system.time(+ zz <- merge( spec.1 = zoo(nmr.spectra.serum[[1]]$V2,
nmr.spectra.serum[[1]]$V1),
+        spec.2 = zoo(nmr.spectra.serum[[2]]$V2, nmr.spectra.serum[[2]]$V1),
fill=NA )
+ )
[1] 0.74 0.07 0.82   NA   NA> system.time(+ ww <- merge(nmr.spectra.serum[[1]], nmr.spectra.serum[[2]],
by="V1",
all=T, sort=T)
+ )
[1] 6.85 0.05 6.94   NA   NA> head(zz)        spec.1 spec.2
-1322.2 -0.651     NA
-1321.9 -0.266     NA
-1321.7 -0.962     NA
-1321.4 -0.602     NA
-1321.2  0.753     NA
-1320.9  1.212     NA> head(ww)       V1   V2.x V2.y
1 -1322.2 -0.651   NA
2 -1321.9 -0.266   NA
3 -1321.7 -0.962   NA
4 -1321.4 -0.602   NA
5 -1321.2  0.753   NA
6 -1320.9  1.212   NA> 
Thanks again.
-Christos 

-----Original Message-----
From: Gabor Grothendieck [mailto:ggrothendieck at gmail.com] 
Sent: Thursday, February 01, 2007 7:25 PM
To: christos at nuverabio.com
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Lining up x-y datasets based on values of x

The zoo package has a multiway merge with optional zero fill.
Here are two ways:

library(zoo)
merge(x = zoo(x[,2], x[,1]),
      y = zoo(y[,2], y[,1]),
      z = zoo(z[,2], z[,1]),
      fill = 0)

# or

library(zoo)
X <- list(x = x, y = y, z = z)
merge0 <- function(..., fill = 0) merge(..., fill = fill)
do.call("merge0",
lapply(X, function(x) zoo(x[,2], x[,1])))

To get more info on zoo try:

vignette("zoo")

On 2/1/07, Christos Hatzis <christos at nuverabio.com>
wrote:> Hi,
>
> I was wondering if there is a direct approach for lining up 2-column 
> matrices according to the values of the first column.  An example and 
> a brute-force approach is given below:
>
> x <- cbind(1:10, runif(10))
> y <- cbind(5:14, runif(10))
> z <- cbind((-4):5, runif(10))
>
> xx <- seq( min(c(x[,1],y[,1],z[,1])), max(c(x[,1],y[,1],z[,1])), 1) w 
> <- cbind(xx, matrix(rep(0, 3*length(xx)), ncol=3))
>
> w[ xx >= x[1,1] & xx <= x[10,1], 2 ] <- x[,2] w[ xx >=
y[1,1] & xx <=
> y[10,1], 3 ] <- y[,2] w[ xx >= z[1,1] & xx <= z[10,1], 4 ]
<- z[,2]
>
> w
>
> I appreciate any pointers.
>
> Thanks.
>
> Christos Hatzis, Ph.D.
> Nuvera Biosciences, Inc.
> 400 West Cummings Park
> Suite 5350
> Woburn, MA 01801
> Tel: 781-938-3830
> www.nuverabio.com
>
> ______________________________________________
> R-help at stat.math.ethz.ch 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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