In jefferis/p1neurons: Dataset of Drosophila male-specific P1 neurons

This vignette provides some quick sample analysis of P1 neurons, making use of the data in this package and functionality from the nat.* series of packages.

library(nat)
library(p1neurons)
library(knitr)

Data summary

There are r length(p1dps) neurons. The following metdata are available:

kable(head(p1dps))

cluster all neurons

hc=hclustfc(names(p1s))
# convert hclust to dendrogram enabling colouring/labelling
library(dendroextras)
hcd=colour_clusters(hc, k=2)
# change the labels from neuron id to sex
labels(hcd)=with(p1s[labels(hcd)], sex)
plot(hcd)

Plot clusters in 3D

plot neurons in 3D broken into the 2 groups from the initial clustering

nopen3d()
plot3d(hc, k=2)

Now just keep group 2 neurons, the male-specific P1 neurons and recluster. Cut the new clustering at a height of h=1, which generally seems to be close to the definition of neuron type in other contexts.

p1.hc=hclustfc(subset(hc, k=2, group=2))
plot(p1.hc)
clear3d()
table(slice(p1.hc, h=1))
plot3d(p1.hc, h=1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

jefferis/p1neurons documentation built on May 19, 2019, 3:06 a.m.