show_similarity {nat.nblast} | R Documentation |
Display two neurons with segments in the query coloured by similarity
Description
By default, the query neuron will be drawn with its segments shaded from red to blue, with red indicating a poor match to the target segments, and blue a good match.
Usage
show_similarity(
query,
target,
smat = NULL,
cols = colorRampPalette(c("red", "yellow", "cyan", "navy")),
col = "black",
AbsoluteScale = FALSE,
PlotVectors = TRUE,
...
)
Arguments
query |
a neuron to compare and colour. |
target |
the neuron to compare against. |
smat |
a score matrix (if |
cols |
the function to use to colour the segments (e.g.
|
col |
the colour with which to draw the target neuron. |
AbsoluteScale |
logical indicating whether the colours should be
calculated based on the minimum and maximum similarities for the neuron
( |
PlotVectors |
logical indicating whether the vectors of the
|
... |
extra arguments to pass to |
Value
show_similarity
is called for the side effect of drawing the
plot; a vector of object IDs is returned.
See Also
The low level function WeightedNNBasedLinesetMatching
is used to retrieve the scores.
Examples
## Not run:
library(nat)
# Pull out gamma and alpha-beta neurons
gamma_neurons <- subset(kcs20, type=='gamma')
ab_neurons <- subset(kcs20, type=='ab')
# Compare two alpha-beta neurons with similar branching, but dissimilar arborisation
clear3d()
show_similarity(ab_neurons[[1]], ab_neurons[[2]])
# Compare an alpha-beta and a gamma neuron with some similarities and differences
clear3d()
show_similarity(ab_neurons[[1]], gamma_neurons[[3]])
## End(Not run)