Teach xyzmatrix to cope with lower case x,y,z colnames

* includes test and docs

Author: jefferis

R/xform.R

@@ -120,6 +120,9 @@ xyzmatrix.dotprops<-function(x, ...) x$points
 
 #' @method xyzmatrix default
 #' @param y,z separate y and z coordinates
+#' @details Note that \code{xyzmatrix.default} can extract 3d coordinates from a
+#'   a \code{matrix} or \code{data.frame} that \bold{either} has exactly 3
+#'   columns \bold{or} has 3 columns named X,Y,Z or x,y,z.
 #' @rdname xyzmatrix
 #' @export
 xyzmatrix.default<-function(x, y=NULL, z=NULL, ...) {
@@ -130,7 +133,8 @@ xyzmatrix.default<-function(x, y=NULL, z=NULL, ...) {
     x=cbind(x,y,z)
   } else if(is.data.frame(x) || is.matrix(x)){
     if(ncol(x)>3){
-      if(all(xyzn%in%colnames(x))) x=x[,xyzn]
+      matched_cols=match(xyzn, toupper(colnames(x)))
+      if(!any(is.na(matched_cols))) x=x[,matched_cols]
       else stop("Ambiguous column names. Unable to retrieve XYZ data")
     } else if(ncol(x)<3) stop("Must have 3 columns of XYZ data")
   }

man/xyzmatrix.Rd

@@ -35,6 +35,12 @@ data
 Assign xyz elements of neuron or dotprops object. Can also
 handle matrix like objects with columns named X,Y,Z
 }
+\details{
+Note that \code{xyzmatrix.default} can extract 3d
+coordinates from a a \code{matrix} or \code{data.frame}
+that \bold{either} has exactly 3 columns \bold{or} has 3
+columns named X,Y,Z or x,y,z.
+}
 \examples{
 n=Cell07PNs[[1]]
 xyzmatrix(n)<-xyzmatrix(n)

tests/testthat/test-xform.R

@@ -74,6 +74,9 @@ test_that("can extract xyz coords from a matrix",{
   expect_equivalent(xyzmatrix(mx),mx)
   colnames(mx)=c("X","Y","Z")
   expect_equal(xyzmatrix(mx),mx)
+  mx2=mx
+  colnames(mx2)=c("x","y","z")
+  expect_equal(xyzmatrix(mx2),mx)
 
   df=data.frame(X=1:4,Y=2:5,Z=3:6,W=1)
   expect_equal(xyzmatrix(df),data.matrix(df[,1:3]))