label_stats=catmaid_get_label_stats() library(dplyr)#> -#> Attaching package: ‘dplyr’#> The following objects are masked from ‘package:nat’: +#> Attaching package: ‘dplyr’#> The following objects are masked from ‘package:catmaid’: +#> +#> intersect, setdiff, union#> The following object is masked from ‘package:testthat’: +#> +#> matches#> The following objects are masked from ‘package:nat’: #> #> intersect, setdiff, union#> The following objects are masked from ‘package:stats’: #> diff --git a/docs/reference/catmaid_get_neuronnames.html b/docs/reference/catmaid_get_neuronnames.html index 85089aa..364924c 100644 --- a/docs/reference/catmaid_get_neuronnames.html +++ b/docs/reference/catmaid_get_neuronnames.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_get_review_status.html b/docs/reference/catmaid_get_review_status.html index 0e262de..7da682c 100644 --- a/docs/reference/catmaid_get_review_status.html +++ b/docs/reference/catmaid_get_review_status.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_get_treenode_table.html b/docs/reference/catmaid_get_treenode_table.html index b5bc525..f24d83e 100644 --- a/docs/reference/catmaid_get_treenode_table.html +++ b/docs/reference/catmaid_get_treenode_table.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_get_user_list.html b/docs/reference/catmaid_get_user_list.html index aa50a7a..caec4c9 100644 --- a/docs/reference/catmaid_get_user_list.html +++ b/docs/reference/catmaid_get_user_list.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_get_volume.html b/docs/reference/catmaid_get_volume.html index a523f7f..38f46a5 100644 --- a/docs/reference/catmaid_get_volume.html +++ b/docs/reference/catmaid_get_volume.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_get_volumelist.html b/docs/reference/catmaid_get_volumelist.html index 2dcdabc..d451f41 100644 --- a/docs/reference/catmaid_get_volumelist.html +++ b/docs/reference/catmaid_get_volumelist.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_login.html b/docs/reference/catmaid_login.html index b46870d..a945a27 100644 --- a/docs/reference/catmaid_login.html +++ b/docs/reference/catmaid_login.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_parse_url.html b/docs/reference/catmaid_parse_url.html index 01fb636..7f8b5da 100644 --- a/docs/reference/catmaid_parse_url.html +++ b/docs/reference/catmaid_parse_url.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_query_by_name.html b/docs/reference/catmaid_query_by_name.html index 9009e57..49ae1be 100644 --- a/docs/reference/catmaid_query_by_name.html +++ b/docs/reference/catmaid_query_by_name.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_query_connected.html b/docs/reference/catmaid_query_connected.html index 1558caf..f12b641 100644 --- a/docs/reference/catmaid_query_connected.html +++ b/docs/reference/catmaid_query_connected.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_rename_neuron.html b/docs/reference/catmaid_rename_neuron.html index f03231c..82de862 100644 --- a/docs/reference/catmaid_rename_neuron.html +++ b/docs/reference/catmaid_rename_neuron.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_skids.html b/docs/reference/catmaid_skids.html index 781ddea..ced0751 100644 --- a/docs/reference/catmaid_skids.html +++ b/docs/reference/catmaid_skids.html @@ -52,7 +52,7 @@
- - + @@ -121,10 +121,13 @@
Value
Details
If the inputs are numeric or have length > 1 they are assumed - already to be skids and are simply converted to integers. If the input is a - string starting with "name:" or "annotation:" they are used for a query by -
+catmaid_query_by_nameor + already to be skids and are simply converted to integers.If the input is a string starting with "name:" or "annotation:" they are + used for a query by
+catmaid_query_by_nameorcatmaid_query_by_annotation, respectively.If the input is a string that cannot be interpreted as a number but does + not start with "name:" or "annotation:", it is assumed to be an + exact match for an annotation.
Examples
@@ -139,6 +142,8 @@Examp catmaid_skids("annotation:ORN") # but only one that matches this (see regex for details) catmaid_skids("annotation:^ORN$") +# As a special case this looks for an exact match annotation for "ORN" +catmaid_skids("ORN") # }
diff --git a/docs/reference/catmaid_user_history.html b/docs/reference/catmaid_user_history.html index 754e402..fafaec3 100644 --- a/docs/reference/catmaid_user_history.html +++ b/docs/reference/catmaid_user_history.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/catmaid_version.html b/docs/reference/catmaid_version.html index 0c7de0d..3bd8b48 100644 --- a/docs/reference/catmaid_version.html +++ b/docs/reference/catmaid_version.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/connectors.html b/docs/reference/connectors.html index 5ff624b..f56fff4 100644 --- a/docs/reference/connectors.html +++ b/docs/reference/connectors.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/copy_tags_connectors.html b/docs/reference/copy_tags_connectors.html index 7e3885e..8404eed 100644 --- a/docs/reference/copy_tags_connectors.html +++ b/docs/reference/copy_tags_connectors.html @@ -52,7 +52,7 @@
- - + diff --git a/docs/reference/index.html b/docs/reference/index.html index 65f14df..8092847 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -52,7 +52,7 @@
- - + @@ -82,7 +82,7 @@
@@ -104,7 +104,7 @@Reference - version 0.8.1.99 + version 0.9.0
- + diff --git a/docs/reference/plot3d.catmaidneuron.html b/docs/reference/plot3d.catmaidneuron.html index 5a49fdf..87bea9b 100644 --- a/docs/reference/plot3d.catmaidneuron.html +++ b/docs/reference/plot3d.catmaidneuron.html @@ -52,7 +52,7 @@ Programmatic access to the CATMAID API
- - + diff --git a/docs/reference/read.neuron.catmaid.html b/docs/reference/read.neuron.catmaid.html index c41054d..3e8ae9c 100644 --- a/docs/reference/read.neuron.catmaid.html +++ b/docs/reference/read.neuron.catmaid.html @@ -52,7 +52,7 @@
- - + @@ -183,9 +183,9 @@
Examp plot3d(nl) ## Full worked example looking at Olfactory Receptor Neurons -# read in ORNs (using a regex to match their name) +# read in ORNs (using exact match to ORN annotation) # note that use a progress bar drop any failures -orns=read.neurons.catmaid("name:ORN (left|right)", OmitFailures = T, .progress='text') +orns=read.neurons.catmaid("ORN", OmitFailures = T, .progress='text') # Add two extra columns to the attached data.frame # for the Odorant receptor genes and the side of brain diff --git a/docs/reference/read_catmaid_selection.html b/docs/reference/read_catmaid_selection.html index f314ad3..c231d2d 100644 --- a/docs/reference/read_catmaid_selection.html +++ b/docs/reference/read_catmaid_selection.html @@ -52,7 +52,7 @@