neuronlistz ordered by metadata df

R/neuronlistz.R

@@ -7,7 +7,8 @@
 #'
 #' @param zip Path to the zip file
 #' @param patt Optional regex pattern or function to specify a subset of files.
-#' @param df A data.frame of metadata that will be attached to the
+#' @param df A \code{data.frame} of metadata that will be attached to the
+#'   \code{neuronlistz} and will define the order of the objects inside it.
 #' @param ... Additional arguments currently ignored
 #'
 #' @return A \code{\link{neuronlist}} object with additional class
@@ -40,6 +41,7 @@ neuronlistz <- function(zip, patt=NULL, df=NULL, ...) {
     ff=setdiff(ff, dff)
     if(is.null(df))
       df <- read_from_zip(zip, dff, neuron=FALSE)
+
   }
 
   keyfilemap <- if(!is.null(patt)) {
@@ -57,13 +59,17 @@ neuronlistz <- function(zip, patt=NULL, df=NULL, ...) {
   names(keyfilemap)=tools::file_path_sans_ext(basename(keyfilemap))
   if(any(duplicated(names(keyfilemap))))
     stop("keyfilemap must have unique names as elements!")
-
-  nlf=structure(rep(F,length(keyfilemap)),.Names=names(keyfilemap))
-  attr(nlf,'keyfilemap')=keyfilemap
-  if(is.null(df)) {
+  if(!is.null(df) && all(names(keyfilemap) %in% rownames(df))) {
+    # reorder neurons to match supplied data.frame
+    keyfilemap=keyfilemap[intersect(rownames(df), names(keyfilemap))]
+  } else {
+    # make a default data.frame
     df=data.frame(id=names(keyfilemap), stringsAsFactors = FALSE)
     rownames(df)=df[['id']]
   }
+
+  nlf=structure(rep(F,length(keyfilemap)),.Names=names(keyfilemap))
+  attr(nlf,'keyfilemap')=keyfilemap
   attr(nlf,'db')=zip
   class(nlf)=c('neuronlistz','neuronlist',class(nlf))
   data.frame(nlf)=df

tests/testthat/test-neuronlistz.R

@@ -1,20 +1,22 @@
 test_that("neuronlistz works", {
   tf=tempfile(fileext = '.zip')
   on.exit(unlink(tf))
-  write.neurons(Cell07PNs[1:5], tf, format='rds')
-  expect_true(is.neuronlist(nz <- neuronlistz(tf, df=Cell07PNs[,])))
+  write.neurons(rev(Cell07PNs), tf, format='rds', include.data.frame = T)
+  expect_equal(rev(neuronlistz(tf)), Cell07PNs)
+  write.neurons(Cell07PNs, tf, format='rds', include.data.frame = T, Force = T)
+
+  expect_true(is.neuronlist(nz <- neuronlistz(tf)))
   expect_equal(nz[1:5], Cell07PNs[1:5])
 
   tf2=tempfile(fileext = '.zip')
   on.exit(unlink(tf2), add = T)
   skip_if_not_installed('qs')
-  write.neurons(Cell07PNs[1:5], tf2, format='qs', include.data.frame = T)
+  write.neurons(Cell07PNs, tf2, format='qs', include.data.frame = T)
   nz <- neuronlistz(tf2)
-  expect_equal(nz[1:5], Cell07PNs[1:5])
 
-  expect_equal(nvertices(nz), nvertices(Cell07PNs[1:5]))
-  expect_equal(nz[1:5], Cell07PNs[1:5])
-  expect_equal(nz *1, Cell07PNs[1:5])
+  expect_equal(nz[seq_along(nz)], Cell07PNs)
+  expect_equal(nvertices(nz), nvertices(Cell07PNs))
+  expect_equal(nz *1, Cell07PNs)
 
   nz2 <- neuronlistz(tf2, patt = "EBH.*")
   expect_equal(rownames(nz2[,]), c("EBH11R", "EBH20L", "EBH20R"))