diff --git a/_pkgdown.yml b/_pkgdown.yml index 967b361..3a70c46 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -14,6 +14,7 @@ reference: - catmaid_get_compact_skeleton - catmaid_get_treenode_table - catmaid_get_review_status + - catmaid_get_treenodes_detail - title: Names and Annotations desc: Querying, fetching and setting neuron names and annotations contents: @@ -30,6 +31,7 @@ reference: - catmaid_set_labels - catmaid_remove_labels - catmaid_get_label_stats + - nsoma - title: Synaptic Connections desc: Querying and fetching neuronal connectivity information contents: @@ -62,6 +64,10 @@ reference: - catmaid_parse_url - read_catmaid_selection - write_catmaid_selection +- title: Data + desc: Sample data included with the package + contents: + - AV4b1 - title: Low level functions desc: Functions primarily intended for developer use contents: diff --git a/docs/authors.html b/docs/authors.html index 081cd74..7b4afd9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -55,7 +55,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/index.html b/docs/index.html index 6ffe9d9..e3133f5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -32,7 +32,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/news/index.html b/docs/news/index.html index f09098a..cba618d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -55,7 +55,7 @@ catmaid - 0.9.0.9000 + 0.9.1 @@ -98,11 +98,13 @@

Changelog

Source: NEWS.md -
+

-catmaid 0.9.0.9000

+catmaid 0.9.1
diff --git a/docs/reference/catmaid_add_volume.html b/docs/reference/catmaid_add_volume.html index 7b7341d..48d7061 100644 --- a/docs/reference/catmaid_add_volume.html +++ b/docs/reference/catmaid_add_volume.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1
diff --git a/docs/reference/catmaid_connection_setenv.html b/docs/reference/catmaid_connection_setenv.html index 69f6bc5..74fc7db 100644 --- a/docs/reference/catmaid_connection_setenv.html +++ b/docs/reference/catmaid_connection_setenv.html @@ -64,7 +64,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_entities_from_models.html b/docs/reference/catmaid_entities_from_models.html index 81b48e3..1e4ec91 100644 --- a/docs/reference/catmaid_entities_from_models.html +++ b/docs/reference/catmaid_entities_from_models.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_fetch.html b/docs/reference/catmaid_fetch.html index 4ad6a60..0fa636f 100644 --- a/docs/reference/catmaid_fetch.html +++ b/docs/reference/catmaid_fetch.html @@ -60,7 +60,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_annotationlist.html b/docs/reference/catmaid_get_annotationlist.html index 20e3d69..7082aff 100644 --- a/docs/reference/catmaid_get_annotationlist.html +++ b/docs/reference/catmaid_get_annotationlist.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_annotations_for_skeletons.html b/docs/reference/catmaid_get_annotations_for_skeletons.html index 2255630..a26239c 100644 --- a/docs/reference/catmaid_get_annotations_for_skeletons.html +++ b/docs/reference/catmaid_get_annotations_for_skeletons.html @@ -63,7 +63,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_compact_skeleton.html b/docs/reference/catmaid_get_compact_skeleton.html index 8b6d9e1..753e669 100644 --- a/docs/reference/catmaid_get_compact_skeleton.html +++ b/docs/reference/catmaid_get_compact_skeleton.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_connector_table.html b/docs/reference/catmaid_get_connector_table.html index fce9c2a..73f0a52 100644 --- a/docs/reference/catmaid_get_connector_table.html +++ b/docs/reference/catmaid_get_connector_table.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_connectors.html b/docs/reference/catmaid_get_connectors.html index f248715..696a85a 100644 --- a/docs/reference/catmaid_get_connectors.html +++ b/docs/reference/catmaid_get_connectors.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_connectors_between.html b/docs/reference/catmaid_get_connectors_between.html index d6444aa..4267941 100644 --- a/docs/reference/catmaid_get_connectors_between.html +++ b/docs/reference/catmaid_get_connectors_between.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_contributor_stats.html b/docs/reference/catmaid_get_contributor_stats.html index c0ce7f2..77da46f 100644 --- a/docs/reference/catmaid_get_contributor_stats.html +++ b/docs/reference/catmaid_get_contributor_stats.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_label_stats.html b/docs/reference/catmaid_get_label_stats.html index 9e58038..d4c0cbf 100644 --- a/docs/reference/catmaid_get_label_stats.html +++ b/docs/reference/catmaid_get_label_stats.html @@ -30,7 +30,9 @@ - + @@ -58,7 +60,7 @@ catmaid - 0.9.0.9000 + 0.9.1 @@ -104,11 +106,15 @@

Get statistics for all labels in a project from a CATMAID server

-

Get statistics for all labels in a project from a CATMAID server

+

catmaid_get_label_stats returns a data.frame with one row + for every node-tag pair.

+

catmaid_get_all_labels returns a character vector of labels

- 
catmaid_get_label_stats(pid = 1, conn = NULL, ...)
+ 
catmaid_get_label_stats(pid = 1, conn = NULL, ...)
+
+catmaid_get_all_labels(pid = 1, conn = NULL, ...)

Arguments

@@ -158,7 +164,8 @@

Examp arrange(desc(n)) multiple_soma_info = soma_labels %>% - filter(skeletonID%in% multiple_soma$skeletonID) + filter(skeletonID%in% multiple_soma$skeletonID)
head(catmaid_get_all_labels())
#> [1] "ends" "synapse?" "TO LEFT ANTE BRANCH" +#> [4] "TO RIGHT ANTE BRANCH" "synapse onto glia?" "TO RIGHT POST BRANCH"
diff --git a/docs/reference/catmaid_get_neuronnames.html b/docs/reference/catmaid_get_neuronnames.html index 59125ba..fb31be4 100644 --- a/docs/reference/catmaid_get_neuronnames.html +++ b/docs/reference/catmaid_get_neuronnames.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_review_status.html b/docs/reference/catmaid_get_review_status.html index 0d0d1ae..21cff65 100644 --- a/docs/reference/catmaid_get_review_status.html +++ b/docs/reference/catmaid_get_review_status.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_treenode_table.html b/docs/reference/catmaid_get_treenode_table.html index 18841c3..e741d2a 100644 --- a/docs/reference/catmaid_get_treenode_table.html +++ b/docs/reference/catmaid_get_treenode_table.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_treenodes_detail.html b/docs/reference/catmaid_get_treenodes_detail.html index 7d0127a..64eadac 100644 --- a/docs/reference/catmaid_get_treenodes_detail.html +++ b/docs/reference/catmaid_get_treenodes_detail.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_user_list.html b/docs/reference/catmaid_get_user_list.html index 20c7fce..008f034 100644 --- a/docs/reference/catmaid_get_user_list.html +++ b/docs/reference/catmaid_get_user_list.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_volume.html b/docs/reference/catmaid_get_volume.html index 1a368b2..ad956ca 100644 --- a/docs/reference/catmaid_get_volume.html +++ b/docs/reference/catmaid_get_volume.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_get_volumelist.html b/docs/reference/catmaid_get_volumelist.html index 9f012be..7436fc1 100644 --- a/docs/reference/catmaid_get_volumelist.html +++ b/docs/reference/catmaid_get_volumelist.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_login.html b/docs/reference/catmaid_login.html index 7f9c5da..1708261 100644 --- a/docs/reference/catmaid_login.html +++ b/docs/reference/catmaid_login.html @@ -69,7 +69,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_parse_url.html b/docs/reference/catmaid_parse_url.html index ad4ecc2..e3ba6c4 100644 --- a/docs/reference/catmaid_parse_url.html +++ b/docs/reference/catmaid_parse_url.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_query_by_name.html b/docs/reference/catmaid_query_by_name.html index 3b98285..3dd3ca8 100644 --- a/docs/reference/catmaid_query_by_name.html +++ b/docs/reference/catmaid_query_by_name.html @@ -66,7 +66,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_query_connected.html b/docs/reference/catmaid_query_connected.html index ada6571..8e05bfb 100644 --- a/docs/reference/catmaid_query_connected.html +++ b/docs/reference/catmaid_query_connected.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_rename_neuron.html b/docs/reference/catmaid_rename_neuron.html index 8f2aee2..562a404 100644 --- a/docs/reference/catmaid_rename_neuron.html +++ b/docs/reference/catmaid_rename_neuron.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_skids.html b/docs/reference/catmaid_skids.html index e12e3dd..0c6b456 100644 --- a/docs/reference/catmaid_skids.html +++ b/docs/reference/catmaid_skids.html @@ -59,7 +59,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_user_history.html b/docs/reference/catmaid_user_history.html index d4f1f3f..154fa17 100644 --- a/docs/reference/catmaid_user_history.html +++ b/docs/reference/catmaid_user_history.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/catmaid_version.html b/docs/reference/catmaid_version.html index e70ebe0..55e1520 100644 --- a/docs/reference/catmaid_version.html +++ b/docs/reference/catmaid_version.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/connectors.html b/docs/reference/connectors.html index 258f03d..89ab119 100644 --- a/docs/reference/connectors.html +++ b/docs/reference/connectors.html @@ -60,7 +60,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/copy_tags_connectors.html b/docs/reference/copy_tags_connectors.html index 50544a8..3283c30 100644 --- a/docs/reference/copy_tags_connectors.html +++ b/docs/reference/copy_tags_connectors.html @@ -60,7 +60,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 21d9f8f..e43a376 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -55,7 +55,7 @@ catmaid - 0.9.0.9000 + 0.9.1 @@ -163,6 +163,12 @@

catmaid_get_review_status()

+ + + + @@ -224,9 +230,15 @@

catmaid_get_label_stats()

+

catmaid_get_label_stats() catmaid_get_all_labels()

+ + + + @@ -370,6 +382,20 @@

+

Data

+

Sample data included with the package

+ +

+ + + + +

Get review status of neurons from CATMAID

+

catmaid_get_treenodes_detail()

+

Fetch position and other information for arbitrary treenode ids

Get statistics for all labels in a project from a CATMAID server

+

nsoma()

+

Return the number of explicitly tagged somata in a (CATMAID) neuron
+

AV4b1

+

A sample CATMAID neuron (from the adult lateral horn of class AV4b1)
@@ -419,6 +445,7 @@

Contents

  • Handling volume meshes
  • CATMAID statistics and users
  • CATMAID URLs and JSON files
    • +
  • Data
  • Low level functions
    • diff --git a/docs/reference/nsoma.html b/docs/reference/nsoma.html new file mode 100644 index 0000000..ece3ee5 --- /dev/null +++ b/docs/reference/nsoma.html @@ -0,0 +1,211 @@ + + + + + + + + +Return the number of explicitly tagged somata in a (CATMAID) neuron — nsoma • catmaid + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Return the number of explicitly tagged somata in a (CATMAID) neuron

    + Source: R/catmaid_nat.R + +
    + +
    + +

    Return the number of explicitly tagged somata in a (CATMAID) neuron

    + +
    + + 
    nsoma(x, ...)
+
+# S3 method for neuronlist
+nsoma(x, ...)
+
+# S3 method for neuron
+nsoma(x, ...)
+
+# S3 method for default
+nsoma(x, soma_label = "soma", ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    x

    Objects to count somata e.g. one or more neurons or a specifier +passed to catmaid_skids

    ...

    Additional arguments, eventually passed by nsoma.default to +catmaid_skids, otherwise ignored.

    soma_label

    Character vector of one or more label names that identify +somata.

    + +

    Value

    + +

    A named integer vector corresponding to the number of neurons + specified by x.

    + +

    Details

    + +

    These functions can cope with loaded neuron objects or CATMAID skid + specifications (see catmaid_skids). Note that this function + will return 0 for any neuron that does not contain a tags$soma + entry, including regular neuron objects .

    + + +

    Examples

    + 
    nsoma(Cell07PNs)
    #> EBH11R EBH20L EBH20R EBI12L EBI22R EBJ23L  EBJ3R EBN19L EBO15L EBO53L ECA34L 
+#>      0      0      0      0      0      0      0      0      0      0      0 
+#>  ECB3L  LI23L  LIC2R   LJ5L   MC3B  MH16L  MM14L   NA7L  NH15L  NH29B  NI16L 
+#>      0      0      0      0      0      0      0      0      0      0      0 
+#>  NIA8L  NIA8R  NNA9L  NNC4R  NNE1L  OFD2L  OKC9R  SDD8L  SH21L  SL20L  TKC8R 
+#>      0      0      0      0      0      0      0      0      0      0      0 
+#>   TL4R   TS7L  TT27R  VA15R  VA20R  VB37L  VB58L 
+#>      0      0      0      0      0      0      0 
    data("AV4b1")
+nsoma(AV4b1)
    #> [1] 1
    nsoma("ORN PNs")
    #> 
+#>  3486381  8021456  4354933  4493199  4651929  7843730  8399890  7515491 
+#>        1        1        1        1        1        1        1        1 
+#>  7092417  7107433  7198338  7852250  7845346  7851153  7864823  7865652 
+#>        1        1        1        1        1        1        1        1 
+#>  7865696  7865767  7873135  7916593  7934904  7935088  8140109  8243455 
+#>        1        1        1        1        1        1        1        1 
+#>  8244723  8244823  8245014  8245146  8245513  8245692  8245869  8246081 
+#>        1        1        1        1        1        1        1        1 
+#>  8246750  8247451  8248631  8252067  8253413  8256186 11279244 13589251 
+#>        1        1        1        1        1        1        1        1 
+#> 14604028 16259595 
+#>        1        1 
    # NOT RUN {
+nsoma(3486381)
+# }
    +
    + +
    + +
    +
    +

    Developed by Gregory Jefferis.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/plot3d.catmaidneuron.html b/docs/reference/plot3d.catmaidneuron.html index c2ec228..4e80d2a 100644 --- a/docs/reference/plot3d.catmaidneuron.html +++ b/docs/reference/plot3d.catmaidneuron.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/read.neuron.catmaid.html b/docs/reference/read.neuron.catmaid.html index 699089b..ec63ab3 100644 --- a/docs/reference/read.neuron.catmaid.html +++ b/docs/reference/read.neuron.catmaid.html @@ -60,7 +60,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/read_catmaid_selection.html b/docs/reference/read_catmaid_selection.html index c4afc99..3cd5899 100644 --- a/docs/reference/read_catmaid_selection.html +++ b/docs/reference/read_catmaid_selection.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1 diff --git a/docs/reference/write_catmaid_selection.html b/docs/reference/write_catmaid_selection.html index e5f2b09..5142f4a 100644 --- a/docs/reference/write_catmaid_selection.html +++ b/docs/reference/write_catmaid_selection.html @@ -58,7 +58,7 @@ catmaid - 0.9.0.9000 + 0.9.1