From 2b4592ebe4a46ea55c0ffa10d007d0d3695bb897 Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Fri, 31 Jul 2020 09:15:13 +0100
Subject: [PATCH] Apply threshold to ROIweight

* the cypher got a bit hairy so I actually only apply the ROI weight threshold to downloaded data.
* I'm sure there must be a way to apply it on the server in a multi-level query.
---
 R/connectivity.R                   | 12 +++++++++---
 man/neuprint_connection_table.Rd   |  3 ++-
 tests/testthat/test-connectivity.R |  9 +++++++++
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/R/connectivity.R b/R/connectivity.R
index e8a7960d..dd71a97b 100644
--- a/R/connectivity.R
+++ b/R/connectivity.R
@@ -103,7 +103,8 @@ neuprint_get_adjacency_matrix <- function(bodyids=NULL, inputids=NULL,
 #' @param by.roi logical, whether or not to break neurons' connectivity down by
 #'   region of interest (ROI)
 #' @param threshold Only return partners >= to an integer value. Default of 1
-#'   returns all partners.
+#'   returns all partners. This threshold will be applied to the ROI weight when
+#'   the \code{roi} argument is specified, otherwise to the whole neuron.
 #' @param superLevel When \code{by.roi=TRUE}, should we look at low-level ROIs
 #'   (\code{superLevel=FALSE}) or only super-level ROIs
 #'   (\code{superLevel=TRUE}). A super-level ROIs can contain multiple
@@ -261,13 +262,18 @@ neuprint_connection_table <- function(bodyids,
   if(!is.null(roi)){
     d <- d[d$roi%in%roi,]
   }
-  if(by.roi&is.null(roi)){
+  if(by.roi && is.null(roi)){
     rois <- neuprint_ROIs(superLevel = superLevel)
     d <- d[d$roi%in%rois,]
   }
   d <-  d[order(d$weight,decreasing=TRUE),]
   rownames(d) <- NULL
-  d[,sort(colnames(d))]
+  d=d[,sort(colnames(d))]
+
+  if(!is.null(roi) && threshold>1)
+    d=d[d$ROIweight>=threshold,]
+
+  d
 }
 
 #' @title Get the common synaptic partners for a set of neurons
diff --git a/man/neuprint_connection_table.Rd b/man/neuprint_connection_table.Rd
index 2a1e9e8b..2ef36202 100644
--- a/man/neuprint_connection_table.Rd
+++ b/man/neuprint_connection_table.Rd
@@ -33,7 +33,8 @@ inputs) or \code{POST}: postsynaptic (downstream outputs) to the given
 region of interest (ROI)}
 
 \item{threshold}{Only return partners >= to an integer value. Default of 1
-returns all partners.}
+returns all partners. This threshold will be applied to the ROI weight when
+the \code{roi} argument is specified, otherwise to the whole neuron.}
 
 \item{superLevel}{When \code{by.roi=TRUE}, should we look at low-level ROIs
 (\code{superLevel=FALSE}) or only super-level ROIs
diff --git a/tests/testthat/test-connectivity.R b/tests/testthat/test-connectivity.R
index 48851025..436eb922 100644
--- a/tests/testthat/test-connectivity.R
+++ b/tests/testthat/test-connectivity.R
@@ -28,6 +28,15 @@ test_that("neuprint_connection_table works", {
             'data.frame')
   # equivalent so we don't worry about rownames
   expect_equivalent(subset(t2, roi=='LH(R)'), t3)
+  expect_equivalent(
+    neuprint_connection_table(
+      c(818983130, 1796818119),
+      prepost = "POST",
+      roi = "LH(R)",
+      threshold = 3
+    ),
+    subset(t3, ROIweight >= 3)
+  )
 })
 
 test_that("other connectivity functions work", {