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[ENH] neuprint_get_adjacency_matrix with neurotransmitters #159

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[ENH] neuprint_get_adjacency_matrix with neurotransmitters #159

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cbc3a62
neurotransmitter filtering added to neuprint_get_adjacency_matrix
dokato Jun 16, 2022
ae5ecd1
fix tets in neurotransmitter filtering added to neuprint_get_adjacenc…
dokato Jun 16, 2022
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12 changes: 12 additions & 0 deletions R/connectivity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
#' alternative to \code{bodyids})
#' @param threshold Return only connections greater than or equal to the
#' indicated strength (default 1 returns all connections).
#' @param neurotransmitter Return only connections with given neurotransmitter
#' type.
#' @param sparse Whether to return a sparse adjacency matrix (of class
#' \code{\link[=CsparseMatrix-class]{CsparseMatrix}}). This may be a
#' particularly good idea for large matrices of >5000 neurons, especially if a
Expand Down Expand Up @@ -58,6 +60,7 @@
neuprint_get_adjacency_matrix <- function(bodyids=NULL, inputids=NULL,
outputids=NULL,
threshold=1L,
neurotransmitter=NULL,
dataset = NULL,
chunksize=1000L,
all_segments = FALSE, conn = NULL,
Expand Down Expand Up @@ -110,8 +113,17 @@ neuprint_get_adjacency_matrix <- function(bodyids=NULL, inputids=NULL,
all_segments.json = ifelse(all_segments,"Segment","Neuron")
namefield=neuprint_name_field(conn=conn, dataset=dataset)
checkmate::assertIntegerish(threshold, lower = 1, len = 1, any.missing = F)
if (!is.null(neurotransmitter)) {
checkmate::assertChoice(neurotransmitter, c("acetylcholine", "gaba", "glutamate"))
nt_filter <- glue(paste(
"MATCH (n:`{all_segments.json}`) WHERE n.{neurotransmitter} >= n.acetylcholine AND n.{neurotransmitter} >= n.gaba AND n.{neurotransmitter} >= n.glutamate AND n.{neurotransmitter} >= n.neither",
"MATCH (m:`{all_segments.json}`) WHERE m.{neurotransmitter} >= m.acetylcholine AND m.{neurotransmitter} >= m.gaba AND m.{neurotransmitter} >= m.glutamate AND m.{neurotransmitter} >= m.neither"
))
} else
nt_filter <- ""
cypher = glue(
"WITH {id2json(inputids)} AS input, {id2json(outputids)} AS output",
nt_filter,
"MATCH (n:`{all_segments.json}`)-[c:ConnectsTo]->(m)",
"WHERE n.bodyId IN input AND m.bodyId IN output",
ifelse(threshold>1, paste("AND c.weight>",threshold-1),""),
Expand Down
4 changes: 4 additions & 0 deletions man/neuprint_get_adjacency_matrix.Rd
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2 changes: 2 additions & 0 deletions tests/testthat/test-connectivity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,8 @@ test_that("other connectivity functions work", {
expect_equal(rownames(t1), rownames(t2))
expect_true(length(t1)>0)

expect_error(neuprint_get_adjacency_matrix(bodyids = da2s$bodyid, neurotransmitter = "x"))

expect_is(t3 <- neuprint_simple_connectivity(da2s$bodyid[1], prepost='PRE'),
'data.frame')
pns11=neuprint_search('.*PN.*', meta=FALSE, all_segments = FALSE)[1:11]
Expand Down