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Fix/neuprint bodies in roi #79

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Feb 11, 2020
Merged

Fix/neuprint bodies in roi #79

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7b5422f
fox neuprint_bodies_in_ROI
jefferis Feb 9, 2020
88e8eca
Add example and test
jefferis Feb 9, 2020
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14 changes: 10 additions & 4 deletions R/roi.R
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Original file line number Diff line number Diff line change
Expand Up @@ -52,18 +52,24 @@ neuprint_find_neurons <- function(input_ROIs,

#' @export
#' @rdname neuprint_find_neurons
#' @examples
#' \donttest{
#' lhr=neuprint_bodies_in_ROI('LH(R)')
#' head(lhr)
#' }
neuprint_bodies_in_ROI <- function(roi, dataset = NULL, all_segments = FALSE, conn = NULL, ...){
all_segments = ifelse(all_segments,"Segment","Neuron")
roicheck = neuprint_check_roi(rois=roi, dataset = dataset, conn = conn, ...)
cypher = sprintf("MATCH (n :`%s`) WHERE n.%s WITH n AS n, apoc.convert.fromJsonMap(n.roiInfo) AS roiInfo RETURN n.bodyId AS bodyid, n.size AS voxels, n.pre, n.post, roiInfo.%s.pre, roiInfo.%s.post",
cypher = sprintf("MATCH (n :`%s`) WHERE n.`%s` WITH n AS n, apoc.convert.fromJsonMap(n.roiInfo) AS roiInfo RETURN n.bodyId AS bodyid, n.size AS voxels, n.pre AS pre, n.post as post, roiInfo.`%s`.pre AS roipre, roiInfo.`%s`.post AS roipost",
all_segments,
roi,
roi,
roi)
nc = neuprint_fetch_custom(cypher=cypher, conn = conn, dataset = dataset, ...)
d = data.frame(do.call(rbind,lapply(nc$data,unlist)))
colnames(d) = unlist(nc$columns)
d
df=neuprint_list2df(nc, return_empty_df = T)
df$roipre[is.na(df$roipre)]=0
df$roipost[is.na(df$roipost)]=0
df
}

#' @title Get the connectivity between ROIs in a neuPrint dataset
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6 changes: 6 additions & 0 deletions tests/testthat/test-roi.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
skip_if(as.logical(Sys.getenv("SKIP_NP_SERVER_TESTS")))

test_that("neuprint_bodies_in_ROI works", {
expect_is(df <- neuprint_bodies_in_ROI('ATL(L)'), 'data.frame')
expect_named(df, c("bodyid", "voxels", "pre", "post", "roipre", "roipost"))
})