R/summary.R
summary.neuron.Rdsummary.neuronlist computes tree statistics for all the
neurons in a neuronlist object
summary.neuron computes statistics for individual neurons
summary.mesh3d computes statistics including face numbers
and surface area for meshes. See vcgArea for details of
area calculation.
summary.dotprops computes statistics for individual
neurons in dotprops format. Note the veclength argument.
# S3 method for neuronlist
summary(object, ..., include.attached.dataframe = FALSE)
# S3 method for neuron
summary(object, ...)
# S3 method for mesh3d
summary(object, ...)
# S3 method for dotprops
summary(object, veclength = 1, ...)The neuron or neuronlist to summarise
For summary.neuronlist additional arguments passed on to
summary methods for individual neurons
Whether to include the neuronlists attached metadata in the returned data.frame.
The vector length to assume for each segment so that a cable length estimate can be made.
A data.frame summarising the tree properties of the neuron
with columns
root
nodes
segments
branchpoints
endpoints
cable.length
nTrees
# summary for a whole neuronlist
summary(Cell07PNs)
#> root nodes segments branchpoints endpoints cable.length nTrees
#> EBH11R 1 180 33 16 18 297.1763 1
#> EBH20L 1 200 26 12 15 327.0929 1
#> EBH20R 1 199 25 12 14 347.6153 1
#> EBI12L 1 169 23 11 13 294.4680 1
#> EBI22R 1 160 27 13 15 303.0150 1
#> EBJ23L 1 156 28 13 16 292.3298 1
#> EBJ3R 1 118 32 15 18 286.0233 1
#> EBN19L 1 162 31 15 17 314.7040 1
#> EBO15L 1 167 39 19 21 350.7743 1
#> EBO53L 1 175 26 12 15 314.9850 1
#> ECA34L 1 446 149 72 78 910.0081 1
#> ECB3L 1 366 124 57 68 936.4803 1
#> LI23L 1 188 29 14 16 236.5884 1
#> LIC2R 1 279 27 13 15 416.1551 1
#> LJ5L 1 154 29 14 16 241.9808 1
#> MC3B 1 118 27 13 15 280.7168 1
#> MH16L 1 171 22 10 13 261.7648 1
#> MM14L 1 216 23 11 13 305.3770 1
#> NA7L 1 121 13 6 8 186.6893 1
#> NH15L 1 83 26 12 15 212.3443 1
#> NH29B 1 101 34 16 19 231.5922 1
#> NI16L 1 122 28 13 16 226.2681 1
#> NIA8L 1 961 32 15 18 387.3223 1
#> NIA8R 1 797 25 12 14 332.0756 1
#> NNA9L 2 2481 171 84 88 991.4211 1
#> NNC4R 2 1902 125 61 65 863.8289 1
#> NNE1L 1 2500 163 78 86 1013.2454 1
#> OFD2L 1 2439 161 77 85 992.2950 1
#> OKC9R 1 2556 144 67 78 1013.5630 1
#> SDD8L 2 2452 151 74 78 1007.6639 1
#> SH21L 1 148 19 9 11 234.8228 1
#> SL20L 1 213 30 14 17 258.2600 1
#> TKC8R 2 605 11 4 8 253.7726 1
#> TL4R 1 135 25 11 15 211.1676 1
#> TS7L 1 176 33 16 18 244.8527 1
#> TT27R 1 168 30 14 17 226.0329 1
#> VA15R 1 147 17 8 10 213.8872 1
#> VA20R 1 160 21 10 12 215.0711 1
#> VB37L 1 162 14 6 9 218.7555 1
#> VB58L 1 154 17 8 10 231.9512 1
# including the attached data.frame with additional metadata
head(summary(Cell07PNs, include.attached.dataframe = FALSE))
#> root nodes segments branchpoints endpoints cable.length nTrees
#> EBH11R 1 180 33 16 18 297.1763 1
#> EBH20L 1 200 26 12 15 327.0929 1
#> EBH20R 1 199 25 12 14 347.6153 1
#> EBI12L 1 169 23 11 13 294.4680 1
#> EBI22R 1 160 27 13 15 303.0150 1
#> EBJ23L 1 156 28 13 16 292.3298 1
# for a single regular format neuron
summary(Cell07PNs[[1]])
#> root nodes segments branchpoints endpoints cable.length nTrees
#> 1 1 180 33 16 18 297.1763 1
# for a single dotprops format neuron
summary(kcs20[[1]])
#> nodes cable.length
#> 1 284 284
# specify a different estimate for the cable length associated with a single
# point in the neuron
summary(kcs20[[1]], veclength=1.2)
#> nodes cable.length
#> 1 284 340.8