From 6c0cc53978d9f2f82c8e71b10b2d8f97276a73fa Mon Sep 17 00:00:00 2001
From: Romain Franconville <romain.franconville@protonmail.com>
Date: Wed, 15 Jan 2020 11:28:11 -0500
Subject: [PATCH 1/2] Fixed common_connectivity. Also got faster because we're
 only looping through the actual common connections

---
 R/connectivity.R | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/connectivity.R b/R/connectivity.R
index 38a941e4..347db309 100644
--- a/R/connectivity.R
+++ b/R/connectivity.R
@@ -135,20 +135,20 @@ neuprint_common_connectivity <- function(bodyids, statuses = NULL,
                             all_segments))
   class(Payload) = "json"
   com.conn = neuprint_fetch(path = 'api/npexplorer/commonconnectivity', body = Payload, conn = conn, ...)
-  m = matrix(0,nrow = length(bodyids),ncol = length(com.conn$data[[1]][[1]]))
-  rownames(m) = paste0(bodyids,"_weight")
-  connected = c()
-  for(i in 1:length(com.conn$data[[1]][[1]])){
-    s = com.conn$data[[1]][[1]][[i]]
-    find = match(names(s),rownames(m))
-    add = find[!is.na(find)]
-    m[add,i] = unlist(s)[!is.na(find)]
-    connected = c(connected,ifelse(is.null(s$input),s$output,s$input))
+  partnerType <- ifelse(prepost=="PRE","output","input")
+  partnerNames <- sapply(com.conn$data[[1]][[1]],function(d) d[[partnerType]])
+  partnerCount <- table(partnerNames)
+  commonPartners <- names(partnerCount[partnerCount == length(bodyids)])
+  m <-  matrix(0,nrow = length(bodyids),ncol = length(commonPartners))
+  rownames(m) <-  paste0(bodyids,"_weight")
+  colnames(m) <-  commonPartners
+  comData <- com.conn$data[[1]][[1]][which(partnerNames %in% commonPartners)]
+  for(i in 1:length(comData)){
+    s <-  comData[[i]]
+    rName <- names(s)[names(s) %in% rownames(m)]
+    m[rName,as.character(s[[partnerType]])] <- s[[rName]]
   }
-  m = t(apply(m,1,as.numeric))
-  colnames(m) = connected
-  rownames(m) = bodyids
-  m = m[,apply(m,2,function(x) sum(x==0)==0)]
+  rownames(m) <-  bodyids
   m
 }
 

From a657ffb880f0fd23cc6e0507240ca30ac52d4fe9 Mon Sep 17 00:00:00 2001
From: Romain Franconville <romain.franconville@protonmail.com>
Date: Wed, 15 Jan 2020 11:32:35 -0500
Subject: [PATCH 2/2] Small fix (in case they are no common partners)

---
 R/connectivity.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/connectivity.R b/R/connectivity.R
index 347db309..e8547a46 100644
--- a/R/connectivity.R
+++ b/R/connectivity.R
@@ -143,8 +143,8 @@ neuprint_common_connectivity <- function(bodyids, statuses = NULL,
   rownames(m) <-  paste0(bodyids,"_weight")
   colnames(m) <-  commonPartners
   comData <- com.conn$data[[1]][[1]][which(partnerNames %in% commonPartners)]
-  for(i in 1:length(comData)){
-    s <-  comData[[i]]
+
+  for(s in comData){
     rName <- names(s)[names(s) %in% rownames(m)]
     m[rName,as.character(s[[partnerType]])] <- s[[rName]]
   }