flywire_ntplot: Plot neurotransmitter prediction summaries or synapses in 3D

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Plot neurotransmitter prediction summaries or synapses in 3D

Description

flywire_ntplot plots a ggplot2 histogram of predicted neurotransmitter vs prediction probability.

flywire_ntplot3d makes a 3D plot of synapse location

Usage

flywire_ntplot(
  x,
  nts = c("gaba", "acetylcholine", "glutamate", "octopamine", "serotonin", "dopamine",
    "neither"),
  cleft.threshold = 0,
  local = NULL,
  cloudvolume.url = NULL
)

flywire_ntplot3d(
  x,
  nts = c("gaba", "acetylcholine", "glutamate", "octopamine", "serotonin", "dopamine"),
  plot = c("points", "spheres"),
  cleft.threshold = 0,
  local = NULL,
  cloudvolume.url = NULL,
  ...
)

Arguments

x	A flywire rootid or a data.frame of neurotransmitter predictions returned by flywire_ntpred
nts	A character vector of neurotransmitters to include in the plot (default all 6)
cleft.threshold	A threshold for the cleft score calculated by Buhmann et al 2019 (default 0, we have used 30-100 to increase specificity)
local	path to SQLite synapse data. Evaluated by fafbseg:::local_or_google. Work in progress. Default is to download this data and place it in ~/projects/JanFunke.
cloudvolume.url	The segmentation source URL for cloudvolume. Normally you can ignore this and rely on the default segmentation chosen by choose_segmentation
plot	Whether to plot points or spheres ("points" with size=5 works quite well)
...	additional arguments passed to spheres3d or points3d

Value

flywire_ntplot returns a ggplot2::ggplot object that can be further customised to modify the plot (see examples).

See Also

Other automatic-synapses: flywire_adjacency_matrix(), flywire_neurons_add_synapses(), flywire_ntpred(), flywire_partners()

Examples

# a cholinergic olfactory projection neuron
ntp=flywire_ntpred("720575940615237849")
flywire_ntplot(ntp)
flywire_ntplot(ntp, nts=c("gaba", "acetylcholine", "glutamate"))
flywire_ntplot(ntp, nts=c("gaba", "acetylcholine", "glutamate"), cleft.threshold=100)

# ids for several Kenyon cells
kcsel=c("720575940623755722", "720575940609992371", "720575940625494549",
"720575940619442047", "720575940620517656", "720575940609793429",
"720575940617265029", "720575940631869024", "720575940637441955",
"720575940638892789")
kcpreds=flywire_ntpred(kcsel)
# collect the ggplot object
p <- flywire_ntplot(kcpreds)
# print it to see the aggregate plot (all neurons together)
p
# ... or use ggplot facets to separate by query neuron
p+ggplot2::facet_wrap(query~.)

## Not run: 
flywire_ntplot3d(ntp, nts=c("gaba", "acetylcholine",
  "glutamate"), plot='points', cleft.threshold=30, size=5)

## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.