catmaid_get_treenode_table: Return tree node table for a given neuron

In jefferis/rcatmaid: R access to the API for the CATMAID web image annotation tool

Return tree node table for a given neuron

Description

Return tree node table for a given neuron

Usage

catmaid_get_treenode_table(skid, pid = 1, conn = NULL, raw = FALSE, ...)

Arguments

skid	Numeric skeleton id
pid	project id (default 1)
conn	the catmaid_connection object
raw	Whether to return completely unprocessed data (when TRUE) or to convert the nodes and connectors lists into processed data.frames (when FALSE, the default)
...	Additional arguments passed to the catmaid_fetch function.

Value

A data.frame with columns

• id

• parent_id

• confidence

• x

• y

• z

• r

• user_id

• last_modified

• reviewer_id (character vector with comma separated reviewer ids)

In addition two data.frames will be included as attributes: reviews, tags.

See Also

catmaid_get_compact_skeleton, read.neuron.catmaid and catmaid_get_user_list to translate user ids into names.

Examples

## Not run: 
# get tree node table for neuron 10418394
tnt=catmaid_get_treenode_table(10418394)

# look at tags data
str(attr(tnt, 'tags'))
# merge with main node table to get xyz position
tags=merge(attr(tnt, 'tags'), tnt, by='id')
# label up a 3d neuron plot
n=read.neuron.catmaid(10418394)
plot3d(n, WithNodes=F)
text3d(xyzmatrix(tags), texts = tags$tag, cex=.7)

## End(Not run)

jefferis/rcatmaid documentation built on Aug. 16, 2022, 8:52 p.m.