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WIP: added withMeta parameter to nlapply #501

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WIP: added withMeta parameter to nlapply #501

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06010e9
added withMeta parameter to nlapply
dokato Jun 9, 2022
673a945
changed url path for the tests to pass
dokato Jun 9, 2022
ce00451
changed url path to http for the tests to pass
dokato Jun 9, 2022
55c92be
neuronlist test fixed
dokato Jun 9, 2022
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10 changes: 9 additions & 1 deletion R/neuronlist.R
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Original file line number Diff line number Diff line change
Expand Up @@ -388,6 +388,8 @@ as.data.frame.neuronlist<-function(x, row.names = names(x), optional = FALSE, ..
#' error. The default value (\code{NA}) will result in nlapply stopping with
#' an error message the moment there is an error. For other values, see
#' details.
#' @param withMeta whether or not to include the metadata from the neuronlist
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I don't think this is 100% clear yet. I think you need to add something like "in the body of each object in the output list"

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Is the intention that the metadata dataframe should be removed from the output? It is. Maybe this should be signalled.

#' data.frame
#' @param .progress Character vector specifying the type of progress bar (see
#' Progress bar section for details) The default value of \code{"auto"} shows
#' a progress bar in interactive use after 2s. The default value can be
Expand Down Expand Up @@ -479,7 +481,7 @@ as.data.frame.neuronlist<-function(x, row.names = names(x), optional = FALSE, ..
#' options(nat.progress=NULL)
#' sl=nlapply(Cell07PNs, FUN = seglengths)
#' }
nlapply<-function (X, FUN, ..., subset=NULL, OmitFailures=NA,
nlapply<-function (X, FUN, ..., subset=NULL, OmitFailures=NA, withMeta=FALSE,
.progress=getOption('nat.progress', default='auto')){
if(isTRUE(.progress=='auto')) {
.progress = ifelse(interactive(), "natprogress", "none")
Expand All @@ -495,6 +497,12 @@ nlapply<-function (X, FUN, ..., subset=NULL, OmitFailures=NA,
class(X)
else c("neuronlist", 'list')

if (withMeta && ncol(X[,]) > 0) {
meta_list <- split(X[,], seq(nrow(X[,])))
Xlist = mapply(append, X, meta_list, SIMPLIFY = FALSE)
X = as.neuronlist(lapply(Xlist, as.neuron))
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This doesn't work if X contains dotprops rather than neuron objects. I think you need to set the class based on the class of each element of X before appending. I guess you have to use append in case your metadata overwrites one of the existing fields in the elements of X? NB I have tried to avoid assuming that every element of a neuronlist has the same class.

}

if(!is.null(subset)){
if(!is.character(subset)) subset=names(X)[subset]
Y=X
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2 changes: 1 addition & 1 deletion R/neuronlistfh.R
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Expand Up @@ -655,7 +655,7 @@ remotesync.default<-function(x, remote=attr(x,'remote'), download.missing=TRUE,
#' @rdname remotesync
#' @examples
#' \dontrun{
#' kcs20=read.neuronlistfh('http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/kcs20.rds')
#' kcs20=read.neuronlistfh('http://virtualflybrain.org/data/VFB/nblast/flycircuit/kcs20.rds')
#' # update object from the web
#' kcs20=remotesync(kcs20)
#' # download all neurons with significant innervation of the vertical lobe
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4 changes: 4 additions & 0 deletions man/nlapply.Rd
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2 changes: 1 addition & 1 deletion man/remotesync.Rd
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4 changes: 2 additions & 2 deletions tests/testthat/test-.neuronlistfh-remote-nocran.R
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Expand Up @@ -6,7 +6,7 @@ test_that("we can download a neuronlistfh object with MD5'd objects", {
localdir <- tempfile()
dir.create(localdir)
on.exit(unlink(localdir, recursive=TRUE))
kcs20.url="http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/kcs20.rds"
kcs20.url="http://virtualflybrain.org/data/VFB/nblast/flycircuit/kcs20.rds"
kcs20md5 <- read.neuronlistfh(kcs20.url, localdir=localdir, quiet=TRUE)
# test trying to read in neuronlistfh object which is now available locally
# before we have downloaded any data objects
Expand All @@ -26,7 +26,7 @@ test_that("we can synchronise a neuronlistfh object with its remote", {
localdir <- tempfile()
dir.create(localdir)
on.exit(unlink(localdir, recursive=TRUE))
kcs20fh.remote <- read.neuronlistfh("http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/kcs20.rds",
kcs20fh.remote <- read.neuronlistfh("http://virtualflybrain.org/data/VFB/nblast/flycircuit/kcs20.rds",
localdir=localdir)
expect_equal(dim(kcs20fh.remote[[1]]$points), c(284, 3))
# make a neuronlistfh object from the local data bundled with this package
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18 changes: 18 additions & 0 deletions tests/testthat/test-neuronlist.R
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Expand Up @@ -327,6 +327,24 @@ test_that("[<-.neuronlist does the right thing",{
expect_null(colnames(kcs13[,]<-NULL))
})

test_that("neuronlist includes metadata",{
kcs13=kcs20[1:3]

# expect that withMeta output will contain more attributes
out1 = nlapply(kcs13, function(x) x)
out2 = nlapply(kcs13, function(x) x, withMeta = T)
expect_true(
length(attributes(out1[[2]])$names) < length(attributes(out2[[2]])$names)
)
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I'm not sure this was the intention:

> out1
'neuronlist' containing 3 'dotprops' objects and 'data.frame' with 14 vars [75.9 kB]
> out2
'neuronlist' containing 3 'list' objects and 'data.frame' with 0 vars [94.5 kB]


# or parts of columns
data.frame(kcs13) <- NULL
out3 = nlapply(kcs13, function(x) x, withMeta = T)
expect_true(
all(names(out1[[1]]) == names(out3[[1]]))
)
})

test_that("prune twigs of a neuronlist", {
n = Cell07PNs[1:3]

Expand Down