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hemibrain_compartment_metrics doesn't return what it says #27

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jefferis opened this issue Oct 6, 2020 · 2 comments
Open

hemibrain_compartment_metrics doesn't return what it says #27

jefferis opened this issue Oct 6, 2020 · 2 comments
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@jefferis
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jefferis commented Oct 6, 2020

> hcm = hemibrain_compartment_metrics(neurons,
+ resample = NULL,
+ just.leaves = TRUE, # just look how much the leaves of skeletons overlap, quicker (default)
+ delta = 5)
> hcm
               bodyid pre post upstream downstream status    statusLabel cropped
1702323386 1702323386 371 4753     4753       2165 Traced Roughly traced   FALSE
2068966051 2068966051 104 1619     1619        683 Traced         Leaves    TRUE
2069311379 2069311379  11  466      466         61 Traced         Leaves    TRUE
1702305987 1702305987 612 2116     2116       2487 Traced Roughly traced   FALSE
5812996027 5812996027 232  714      714       1595 Traced Roughly traced   FALSE
                          name    type cellBodyFiber     voxels
1702323386                <NA>    <NA>          <NA> 1600207841
2068966051                <NA>    <NA>          <NA>  314685458
2069311379                <NA>    <NA>          <NA>  147761931
1702305987 lLN2R_b(Regional)_R lLN2R_b         AVM02  806128911
5812996027            lLN12b_R  lLN12B         AVM02  368364508
                                      notes  soma total.outputs total.inputs
1702323386                             <NA> FALSE          2165         4753
2068966051                             <NA> FALSE           683         1619
2069311379                             <NA> FALSE            61          466
1702305987 AL-LN2L (Tanaka et al. JCN 2012)  TRUE          2487         2116
5812996027                             <NA>  TRUE          1595          714
           axon.outputs dend.outputs axon.inputs dend.inputs total.outputs.density
1702323386            0          807           0        1394            0.36084107
2068966051          256          393         684         935            0.23093998
2069311379           34           13         184         116            0.05028509
1702305987            0         2003           5        1723            0.61605712
5812996027          643          952         120         591            0.99917822
           total.inputs.density axon.outputs.density dend.outputs.density
1702323386            0.7921836           0.00000000           0.40420018
2068966051            0.5474258           0.21063130           0.23878459
2069311379            0.3841451           0.07703632           0.04169616
1702305987            0.5241564           0.00000000           0.63396725
5812996027            0.4472810           1.86887198           0.80502580
           axon.inputs.density dend.inputs.density total.length  axon.length
1702323386           0.0000000           0.6982095     5999.871    0.1357645
2068966051           0.5627805           0.5681007     2957.478 1215.3939068
2069311379           0.4169024           0.3720580     1213.083  441.3502511
1702305987           0.3576827           0.5453448     4036.963   13.9788682
5812996027           0.3487786           0.4997587     1596.312  344.0578089
           dend.length pd.length segregation_index
1702323386   1996.5355 28.282945                NA
2068966051   1645.8349 26.161610                NA
2069311379    311.7793 33.592591                NA
1702305987   3159.4692  2.623717                NA
5812996027   1182.5708 19.392830                NA
@jefferis
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jefferis commented Oct 6, 2020

In the example for this function, this step fails:

hist(hcm$overlap_locality, breaks = 100)
Error in hist.default(hcm$overlap_locality, breaks = 100) : 
     'x' must be numeric
   Calls: hist -> hist.default

@jefferis
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jefferis commented Oct 6, 2020

That's because there is no column called overlap_locality.

jefferis added a commit that referenced this issue Oct 6, 2020
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