From 6c4f0e3618f1aa686b2dcbe403c76185b70c0fc2 Mon Sep 17 00:00:00 2001 From: alexanderbates Date: Tue, 22 Oct 2024 21:17:34 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20flyconne?= =?UTF-8?q?ctome/bancr@c7c0807583aeb91a16e3b2715f7eefcbeb58ce1c=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.surf.html | 6 ++-- reference/banc_brain_neuropils.surf.html | 8 +++++ reference/banc_cave_query.html | 13 ++++---- reference/banc_cellid_from_segid.html | 12 +++++-- reference/banc_decapitate.html | 14 +++++++- reference/banc_islatest.html | 2 +- reference/banc_latestid.html | 2 +- reference/banc_neuron_comparison_plot.html | 4 +-- reference/banc_read_neuron_meshes.html | 31 +++++++++++++++--- reference/banc_rootid.html | 12 ++++++- reference/banc_scene.html | 18 +++++++--- reference/bancsee.html | 8 ++++- reference/banctable_query.html | 38 +++++++++++++++++----- reference/dr_banc.html | 6 ++-- reference/index.html | 6 ++-- search.json | 2 +- 17 files changed, 140 insertions(+), 44 deletions(-) create mode 100644 reference/banc_brain_neuropils.surf.html diff --git a/pkgdown.yml b/pkgdown.yml index f7df05d..97c91f6 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-09-19T09:51Z +last_built: 2024-10-22T21:16Z urls: reference: https://flyconnectome.github.io/bancr/reference article: https://flyconnectome.github.io/bancr/articles diff --git a/reference/banc.surf.html b/reference/banc.surf.html index e59e98e..5e9b971 100644 --- a/reference/banc.surf.html +++ b/reference/banc.surf.html @@ -98,7 +98,7 @@

Usage banc_neck_connective.surf -banc_neuropils.surf +banc_brain_neuropils.surf banc_al.surf @@ -126,13 +126,13 @@

Format<

An object of class hxsurf (inherits from list) of length 4.

An object of class hxsurf (inherits from list) of length 4.

An object of class hxsurf (inherits from list) of length 4.

-

An object of class data.frame with 220 rows and 2 columns.

+

An object of class data.frame with 311 rows and 3 columns.

See also

banc.surf for the available neuropil objects for BANC. These are hxsruf objects, names for subregions can be found as so: -banc_neuropils.surf$RegionList

+banc_brain_neuropil.surf$RegionList

diff --git a/reference/banc_brain_neuropils.surf.html b/reference/banc_brain_neuropils.surf.html new file mode 100644 index 0000000..8c3b0e2 --- /dev/null +++ b/reference/banc_brain_neuropils.surf.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/banc_cave_query.html b/reference/banc_cave_query.html index 51b1d36..961b9fd 100644 --- a/reference/banc_cave_query.html +++ b/reference/banc_cave_query.html @@ -90,15 +90,16 @@

Examples#> #> intersect, setdiff, setequal, union cell_info=banc_cave_query('cell_info') +#> Warning: using default setting +#> Error in py_call_impl(callable, call_args$unnamed, call_args$named) : +#> requests.exceptions.SSLError: HTTPSConnectionPool(host='global.daf-apis.com', port=443): Max retries exceeded with url: /info/api/v2/datastack/full/brain_and_nerve_cord (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available.")) +#> Run `reticulate::py_last_error()` for details. +#> • Please run dr_fafbseg() to help diagnose. +#> Error in (function (datastack_name = getOption("fafbseg.cave.datastack_name", "flywire_fafb_production")) { cavec = check_cave() client = try(cavec$CAVEclient(datastack_name)) if (inherits(client, "try-error")) { ui_todo("\nPlease run dr_fafbseg() to help diagnose.") stop("There seems to be a problem connecting to datastack: ", datastack_name) } client})(datastack_name = datastack_name): There seems to be a problem connecting to datastack: brain_and_nerve_cord cell_info %>% filter(tag2=='anterior-posterior projection pattern') %>% count(tag) -#> # A tibble: 3 × 2 -#> tag n -#> <chr> <int> -#> 1 ascending 2190 -#> 2 descending 1267 -#> 3 intersegmental 16 +#> Error: object 'cell_info' not found # }

diff --git a/reference/banc_cellid_from_segid.html b/reference/banc_cellid_from_segid.html index 87ea24f..d3b964b 100644 --- a/reference/banc_cellid_from_segid.html +++ b/reference/banc_cellid_from_segid.html @@ -143,11 +143,19 @@

See alsoExamples

# \donttest{
 banc_cellid_from_segid(banc_latestid("720575941626035769"))
-#> [1] 1464
+#> Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
+#>   requests.exceptions.SSLError: HTTPSConnectionPool(host='global.daf-apis.com', port=443): Max retries exceeded with url: /info/api/v2/datastack/full/brain_and_nerve_cord (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))
+#> Run `reticulate::py_last_error()` for details.
+#> • Please run dr_fafbseg() to help diagnose.
+#> Error in (function (datastack_name = getOption("fafbseg.cave.datastack_name",     "flywire_fafb_production")) {    cavec = check_cave()    client = try(cavec$CAVEclient(datastack_name))    if (inherits(client, "try-error")) {        ui_todo("\nPlease run dr_fafbseg() to help diagnose.")        stop("There seems to be a problem connecting to datastack: ",             datastack_name)    }    client})(): There seems to be a problem connecting to datastack: brain_and_nerve_cord
 # }
 # \donttest{
 banc_cellid_from_segid(banc_latestid("720575941480769421"))
-#> [1] 224
+#> Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
+#>   requests.exceptions.SSLError: HTTPSConnectionPool(host='global.daf-apis.com', port=443): Max retries exceeded with url: /info/api/v2/datastack/full/brain_and_nerve_cord (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))
+#> Run `reticulate::py_last_error()` for details.
+#> • Please run dr_fafbseg() to help diagnose.
+#> Error in (function (datastack_name = getOption("fafbseg.cave.datastack_name",     "flywire_fafb_production")) {    cavec = check_cave()    client = try(cavec$CAVEclient(datastack_name))    if (inherits(client, "try-error")) {        ui_todo("\nPlease run dr_fafbseg() to help diagnose.")        stop("There seems to be a problem connecting to datastack: ",             datastack_name)    }    client})(): There seems to be a problem connecting to datastack: brain_and_nerve_cord
 # }
diff --git a/reference/banc_decapitate.html b/reference/banc_decapitate.html index 1c0a845..2f6b021 100644 --- a/reference/banc_decapitate.html +++ b/reference/banc_decapitate.html @@ -102,9 +102,21 @@

Examples# DNa02 m = banc_read_neuron_meshes("720575941478275714") #> downloading meshes -#> parsing downloaded meshes +#> cannot import name 'ssl' from 'urllib3.util.ssl_' (/home/runner/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/urllib3/util/ssl_.py) +#> Error: Please install the python cloudvolume package: +#> This should normally work: +#> fafbseg::simple_python('basic') +#> For more details see ?simple_python or the cloud-volume docshttps://github.com/seung-lab/cloud-volume#setup +#> If you have already installed cloudvolume but it is not found +#> then R probably can't find the relevant version of Python +#> Do: +#> usethis::edit_r_environ() +#> to point to the right python +#> e.g. RETICULATE_PYTHON="/opt/miniconda3/envs/r-reticulate/bin/python" m.brain = banc_decapitate(m) +#> Error: object 'm' not found m.vnc = banc_decapitate(m, invert = TRUE) +#> Error: object 'm' not found # } if (FALSE) { # \dontrun{ plot3d(m.brain, col = "red") diff --git a/reference/banc_islatest.html b/reference/banc_islatest.html index 89abfc1..9cdeb11 100644 --- a/reference/banc_islatest.html +++ b/reference/banc_islatest.html @@ -74,7 +74,7 @@

See also

Examples

- 
banc_islatest("648518346473954669")
+    
banc_islatest("720575941520182775")
 #> [1] FALSE
diff --git a/reference/banc_latestid.html b/reference/banc_latestid.html index 725a67e..7ea15ff 100644 --- a/reference/banc_latestid.html +++ b/reference/banc_latestid.html @@ -114,7 +114,7 @@

See also

Examples

if (FALSE) { # \dontrun{
-banc_latestid("648518346473954669")
+banc_latestid("720575941520182775")
 } # }
diff --git a/reference/banc_neuron_comparison_plot.html b/reference/banc_neuron_comparison_plot.html index 78c2b83..a924998 100644 --- a/reference/banc_neuron_comparison_plot.html +++ b/reference/banc_neuron_comparison_plot.html @@ -148,9 +148,9 @@

Examples # Get some neurons to plot banc.meta.dnao1 <- subset(banc.meta, cell_type=="DNa01") -dna01 <- banc_read_neuron_meshes(banc.meta.dnao1$root_id) +dna01 <- banc_read_neuron_meshes(unique(banc.meta.dnao1$root_id)) banc.meta.dnao2 <- subset(banc.meta, cell_type=="DNa02") -dna02 <- banc_read_neuron_meshes(banc.meta.dnao2$root_id) +dna02 <- banc_read_neuron_meshes(unique(banc.meta.dnao2$root_id)) # Simplify neurons to make them easier to plot dna01 <- nat::nlapply(dna01,Rvcg::vcgQEdecim,percent = 0.1) diff --git a/reference/banc_read_neuron_meshes.html b/reference/banc_read_neuron_meshes.html index d740fb7..e69d95e 100644 --- a/reference/banc_read_neuron_meshes.html +++ b/reference/banc_read_neuron_meshes.html @@ -1,5 +1,5 @@ -Read one or more BANC neuron and nuclei meshes — banc_read_neuron_meshes • bancr +Read one or more BANC neuron and nuclei meshes — banc_read_neuron_meshes • bancr Skip to contents @@ -100,13 +100,34 @@

Examples
# \donttest{
 neuron.mesh <- banc_read_neuron_meshes("720575941478275714")
 #>   downloading meshes
-#>   parsing downloaded meshes
+#> cannot import name 'ssl' from 'urllib3.util.ssl_' (/home/runner/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/urllib3/util/ssl_.py)
+#> Error: Please install the python cloudvolume package:
+#> This should normally work:
+#> fafbseg::simple_python('basic')
+#> For more details see ?simple_python or the cloud-volume docshttps://github.com/seung-lab/cloud-volume#setup
+#> If you have already installed cloudvolume but it is not found
+#> then R probably can't find the relevant version of Python
+#> Do:
+#> usethis::edit_r_environ()
+#>  to point to the right python
+#> e.g. RETICULATE_PYTHON="/opt/miniconda3/envs/r-reticulate/bin/python"
 plot3d(neuron.mesh, alpha = 0.1)
+#> Error: object 'neuron.mesh' not found
 nucleus.mesh <- banc_read_nuclei_mesh("72903876004544795")
+#> cannot import name 'ssl' from 'urllib3.util.ssl_' (/home/runner/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/urllib3/util/ssl_.py)
+#> Error: Please install the python cloudvolume package:
+#> This should normally work:
+#> fafbseg::simple_python('basic')
+#> For more details see ?simple_python or the cloud-volume docshttps://github.com/seung-lab/cloud-volume#setup
+#> If you have already installed cloudvolume but it is not found
+#> then R probably can't find the relevant version of Python
+#> Do:
+#> usethis::edit_r_environ()
+#>  to point to the right python
+#> e.g. RETICULATE_PYTHON="/opt/miniconda3/envs/r-reticulate/bin/python"
 plot3d(nucleus.mesh, col = "black")
-
-
-# }
+#> Error: object 'nucleus.mesh' not found
+# }