simple_catmaid_url: Generate a CATMAID URL for a node or connector

Description Usage Arguments Details Value

View source: R/utils.R

Description

Simple method for generating a CATMAID URL pointing to a particular skeleton node or connector

Usage

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simple_catmaid_url(dfrow, skid, sid0 = 5, zoom = 0, conn = FALSE,
  treenode_id = NULL, xyz_columns = c("x", "y", "z"))

Arguments

dfrow

Required; a single data frame row containing columns of xyz coordinates and (optionally) connector_id with CATMAID coordinates and the connector ID

skid

Required; the skid of the active skeleton

sid0

The ID of the desired stack mirror on your CATMAID server. Found by generating a URL within CATMAID and picking out the sid0 param. Defaults to 5.

zoom

The desired zoom level (s0 parameter) of the URL. Defaults to 0.

conn

Whether or not to specify an active connector ID in the URL. Defaults to FALSE.

treenode_id

A specific treenode ID to set as the active node. Useful if you are generating URLs for nodes postsynaptic to a particular skeleton. Will be ignored if conn is set to TRUE.

xyz_columns

A character vector specifying the names of the columns containing x, y, and z coordinates. Defaults to c("x", "y", "z").

Details

Requires the catmaid.server option to be set in .Rprofile

Value

A character string with the CATMAID URL.


fmlove/tracerutils documentation built on Oct. 22, 2018, 1:09 p.m.