Predict the L/R side of points in fish2 space

Applies the fish2 mirror transform to each input point and measures the signed displacement along the mirror (Y) axis before and after transform. The sign indicates which side of the midline the point lies on.

Usage

fish_point_side(
  xyz,
  units = c("nm", "raw", "emraw", "microns"),
  threshold = 5000,
  rval = c("side", "distance")
)

Arguments

xyz

Point coordinates. Anything accepted by xyzmatrix (matrix, data.frame, neuron, neuronlist), a length-3 numeric vector for a single point, or a character vector of comma-separated "x,y,z" strings (the fishr convention for location columns).

units

Units of the input coordinates. "nm" (the default) matches mirror_fish; "raw", "emraw" and "microns" are scaled to nm via fish_coords first.

threshold

Distance from midline below which points are reported as M rather than L or R. Default 5000 nm (~5 \(\mu\)m, ~1% of the y (medio-lateral) extent of the fish2 brain). Set to 0 for all values to be L or R

rval

What to return. "side" (the default) gives a character vector of side labels ("L", "R" or "M"). "distance" gives a signed distance from the midline in nm (always nm, regardless of units), positive on the right, negative on the left.

Value

When rval = "side", a character vector of "L", "R" or "M", one per input point, or NA for bad points. When rval = "distance", a numeric vector of signed distances from the midline in nm.

Details

right-side points have dist = (mirror_y - y)/2 < 0. Points with |dist| <= threshold are reported as midline. If dist==0 and threshold==0 then points will be reported as "R".

See also

mirror_fish

Examples

# known right-side point (raw voxel)
fish_point_side(c(30159, 33753, 6352), units = "raw")
#> [1] "L"

# a small batch in nm
xyz_nm <- rbind(c(482544, 540048,  95280),   # right
                c(482544, 380000,  95280),   # left
                c(735728, 430864,  94620))   # near midline
fish_point_side(xyz_nm)
#> [1] "L" "R" "M"

# signed distance from the midline (always in nm)
fish_point_side(xyz_nm, rval = "distance")
#> [1] -109997.34   47184.62   -1481.66