Given a vector of skeleton IDs, this will find the glomerului associated with PNs, based on annotations in CATMAID.
find_glomeruli(skids, exclude = NULL, method = c("annotation", "name"), ...)
| skids | Required; an |
|---|---|
| exclude | Optional; a vector of glomeruli to exclude (in the format X for glomerulus X, or the full annotation for unknown glomerulus N) |
| method | Optional; indicating whether to use the neuron 'name' or glomerulus 'annotation's. |
| ... | Additional arguments passed to catmaid_* functions. Use this to specify |
A character vector of glomeruli names
Requires the PN to be annotated with glomerulus X or unknown glomerulus N in CATMAID. Annotations of the form glomerulus X
will be prioritised over unknown glomerulus N, and if there are multiples they will be joined together with a forward slash. If there are
no results with either of these annotations, the string "unknown" will be returned in place of a glomerulus.
Note that annotations of the form glomerulus X right|left are not considered.
# \donttest{ find_glomeruli('WTPN2017_uPN_right')#> [1] "VA6" "VL2a" "VC1" "VC3m" "DL2v" "DM5" #> [7] "VC3m" "VA5" "VL2p" "VC3l/VCy" "VA2" "VM5v" #> [13] "VA4" "VM4" "DL4" "VM7v" "D" "VM1" #> [19] "DP1l" "VM3" "DA1" "DM5" "V" "DM3" #> [25] "VM5v" "DL2d" "DM1" "VA7m" "DC3" "DL3" #> [31] "D" "VM5d" "VA7m" "VA1d" "DA4m" "VC4" #> [37] "DA2" "VM5d" "VC5/VM4" "DL5" "DM4" "VM7d" #> [43] "D" "DA4l" "VM3" "VC3l" "VA1d" "VC4" #> [49] "VM7v" "VC2" "DC4" "VC3l" "VM5d" "VA1v" #> [55] "VM2" "VA1v" "DA2" "VM5v" "VM2" "VC4" #> [61] "VA1v" "DM2" "DL2v" "VCx/VM4" "VC5" "VM4" #> [67] "VC5" "DC3" "VA1v" "DM6" "DA1" "VA3" #> [73] "DA1" "DL2d" "DL2d" "DL2d" "DA3" "DA1" #> [79] "VA5" "VA5" "DA1" "DM5" "DC2" "VA7l" #> [85] "DC3" "DA2" "DA2" "DL3" "VL1" "DP1m" #> [91] "DM6" "DA1" "DL2v" "VM5d" "DA3" "DC2" #> [97] "DM2" "DL2v" "DM6" "VL1" "DL3" "VA3" #> [103] "DL3" "VA7m" "V" "VC3m" "VA1d" "DL3" #> [109] "DL2d" "DA1" "DC1" "VM1" "DP1m" "VL2p" #> [115] "VA1v" "DL1" "DA2" "DA1" "VL2a" "VA1v" #> [121] "VL1" "DA1" "VL2a" "DP1m" "DL1" "VM7d"#> [1] "VA6" "VL2a" "VC1" "VC3m" "DL2v" "DM5" "VC3m" #> [8] "VA5" "VL2p" "VC3l" "VA2" "VM5v" "VA4" "VM4" #> [15] "DL4" "VM7v" "D" "VM1" "DP1l" "VM3" "DA1" #> [22] "DM5" "V" "DM3" "VM5v" "DL2d" "DM1" "VA7m" #> [29] "DC3" "DL3" "D" "VM5d" "VA7m" "VA1d" "DA4m" #> [36] "VC4" "DA2" "VM5d" "VC5/VM4" "DL5" "DM4" "VM7d" #> [43] "D" "DA4l" "VM3" "VC3l" "VA1d" "VC4" "VM7v" #> [50] "VC2" "DC4" "VC3l" "VM5d" "VA1v" "VM2" "VA1v" #> [57] "DA2" "VM5v" "VM2" "VC4" "VA1v" "DM2" "DL2v" #> [64] "VM4" "VC5" "VM4" "VC5" "DC3" "VA1v" "DM6" #> [71] "DA1" "VA3" "DA1" "DL2d" "DL2d" "DL2d" "DA3" #> [78] "DA1" "VA5" "VA5" "DA1" "DM5" "DC2" "VA7l" #> [85] "DC3" "DA2" "DA2" "DL3" "VL1" "DP1m" "DM6" #> [92] "DA1" "DL2v" "VM5d" "DA3" "DC2" "DM2" "DL2v" #> [99] "DM6" "VL1" "DL3" "VA3" "DL3" "VA7m" "V" #> [106] "VC3m" "VA1d" "DL3" "DL2d" "DA1" "DC1" "VM1" #> [113] "DP1m" "VL2p" "VA1v" "DL1" "DA2" "DA1" "VL2a" #> [120] "VA1v" "VL1" "DA1" "VL2a" "DP1m" "DL1" "VM7d"find_glomeruli('WTPN2017_uPN_right', method = 'name')#> [1] "VA6" "VL2a" "VC1" "VC3m" "DL2v" "DM5" "VC3m" "VA5" "VL2p" "VC3l" #> [11] "VA2" "VM5v" "VA4" "VM4" "DL4" "VM7v" "D" "VM1" "DP1l" "VM3" #> [21] "DA1" "DM5" "V" "DM3" "VM5v" "DL2d" "DM1" "VA7m" "DC3" "DL3" #> [31] "D" "VM5d" "VA7m" "VA1d" "DA4m" "VC4" "DA2" "VM5d" "VC5" "DL5" #> [41] "DM4" "VM7d" "D" "DA4l" "VM3" "VC3l" "VA1d" "VC4" "VM7v" "VC2" #> [51] "DC4" "VC3l" "VM5d" "VA1v" "VM2" "VA1v" "DA2" "VM5v" "VM2" "VC4" #> [61] "VA1v" "DM2" "DL2v" "VM4" "VC5" "VM4" "VC5" "DC3" "VA1v" "DM6" #> [71] "DA1" "VA3" "DA1" "DL2d" "DL2d" "DL2d" "DA3" "DA1" "VA5" "VA5" #> [81] "DA1" "DM5" "DC2" "VA7l" "DC3" "DA2" "DA2" "DL3" "VL1" "DP1m" #> [91] "DM6" "DA1" "DL2v" "VM5d" "DA3" "DC2" "DM2" "DL2v" "DM6" "VL1" #> [101] "DL3" "VA3" "DL3" "VA7m" "V" "VC3m" "VA1d" "DL3" "DL2d" "DA1" #> [111] "DC1" "VM1" "DP1m" "VL2p" "VA1v" "DL1" "DA2" "DA1" "VL2a" "VA1v" #> [121] "VL1" "DA1" "VL2a" "DP1m" "DL1" "VM7d"# }