From fa387c28c22f86c2e651791fdb01b662ded4ee8d Mon Sep 17 00:00:00 2001 From: alexanderbates Date: Wed, 7 Aug 2024 23:04:45 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20flyconne?= =?UTF-8?q?ctome/bancr@5a9cbfe09e73ae9d5d2573d4451a2da395e2d604=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgdown.yml | 2 +- reference/banc_add_synapses.html | 51 ++++++++++++++++++++++---- reference/banc_read_neuron_meshes.html | 6 +-- search.json | 2 +- 4 files changed, 48 insertions(+), 13 deletions(-) diff --git a/pkgdown.yml b/pkgdown.yml index 47da0ed..8c08a5c 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.0 pkgdown_sha: ~ articles: {} -last_built: 2024-08-06T23:17Z +last_built: 2024-08-07T23:03Z urls: reference: https://flyconnectome.github.io/bancr/reference article: https://flyconnectome.github.io/bancr/articles diff --git a/reference/banc_add_synapses.html b/reference/banc_add_synapses.html index 0bde4ae..76f9792 100644 --- a/reference/banc_add_synapses.html +++ b/reference/banc_add_synapses.html @@ -43,7 +43,15 @@

Add synapses to neuron objects

Usage

- 
banc_add_synapses(x, ...)
+    
banc_add_synapses(
+  x,
+  id = NULL,
+  connectors = NULL,
+  size.threshold = 5,
+  remove.autapses = TRUE,
+  update.id = TRUE,
+  ...
+)
 
 # S3 method for class 'neuron'
 banc_add_synapses(
@@ -52,6 +60,7 @@ 
Usage
   connectors = NULL,
   size.threshold = 5,
   remove.autapses = TRUE,
+  update.id = TRUE,
   ...
 )
 
@@ -62,6 +71,7 @@ 
Usage
   connectors = NULL,
   size.threshold = 5,
   remove.autapses = TRUE,
+  update.id = TRUE,
   ...
 )
 
@@ -72,6 +82,7 @@ 
Usage
   connectors = NULL,
   size.threshold = 5,
   remove.autapses = TRUE,
+  update.id = TRUE,
   ...
 )
@@ -84,16 +95,12 @@

Arguments... -

Additional arguments passed to methods, nat::nlapply

- -
id
-

The root ID of the neuron. If NULL, it uses the ID from the neuron object

+

The root ID of the neuron. If NULL, it uses the ID from the neuron object

connectors
-

A dataframe of synaptic connections. If NULL, it retrieves the data

+

A dataframe of synaptic connections. If NULL, it retrieves the data

size.threshold
@@ -103,6 +110,14 @@

Argumentsremove.autapses

Whether to remove autapses (self-connections)

+ +
update.id
+

Logical, whether or not to use banc_latestid to update the neuron's root_id when fetching synapses.

+ + +
...
+

Additional arguments passed to methods, nat::nlapply

+

Value

@@ -111,7 +126,27 @@

Value

Examples

- + 
if (FALSE) { # \dontrun{
+# Get BANC ID for DNA01
+id <- "720575941572711675"
+id <- banc_latestid(id)
+
+# Get the L2 skeletons
+n <- banc_read_l2skel(id)
+
+# Re-root to soma
+n.rerooted <- banc_reroot(n)
+
+# Add synapse information, stored at n.syn[[1]]$connectors
+n.syn <- banc_add_synapses(n.rerooted)
+
+# Split neuron
+n.split <- hemibrainr::flow_centrality(n.syn)
+
+# Visualise
+banc_neuron_comparison_plot(n.split)
+} # }
+
diff --git a/reference/banc_read_neuron_meshes.html b/reference/banc_read_neuron_meshes.html index 4d6d3b1..5987e3c 100644 --- a/reference/banc_read_neuron_meshes.html +++ b/reference/banc_read_neuron_meshes.html @@ -104,9 +104,9 @@

Examplesplot3d(neuron.mesh, alpha = 0.1) nucleus.mesh <- banc_read_nuclei_mesh("72903876004544795") plot3d(nucleus.mesh, col = "black") - - -# } + + +# }