vignettes/MBweighted.md

In youngser/mbstructure: Semiparametric spectral modeling of the complete larval Drosophila mushroom body connectome

title: "Weighted LSM"

author: "Johns Hopkins University" "University of Cincinnati" "HHMI Janelia Research Campus"

date: '2018-06-20' output: html_document: code_folding: show css: ~/RFolder/pandoc.css fig.path: ~/Dropbox/Worm/Codes/Connectome/MB-figure/ fig_caption: yes fig_height: 7 fig_width: 7 highlight: pygments keep_md: yes number_sections: yes theme: cerulean toc: yes toc_depth: 3 toc_float: no pdf_document: fig_caption: yes keep_tex: yes number_sections: yes editor_options: chunk_output_type: console

.table { width: 40%; }

Data

library(igraph)
library(Matrix)
print(load(url("http://www.cis.jhu.edu/~parky/weightedMB.Rbin")))

# [1] "wg.R" "wg.L"

summary(wg.R$g); image(wg.R$g[], useAbs=FALSE, main="Right")

# IGRAPH b8d1f90 DNWB 213 7536 -- 
# + attr: name (v/c), type (v/c), claw (v/n), dist (v/n), weight
# | (e/n)

summary(wg.L$g); image(wg.L$g[], useAbs=FALSE, main="Left")

# IGRAPH 462dff7 DNWB 209 9045 -- 
# + attr: name (v/c), type (v/c), claw (v/n), dist (v/n), weight
# | (e/n)

head(wg.R$vdf)

v type claw dist age

Thermo KC A_Right - Mushroom Body Left #4229950 KC 2 337.6380 mature KC12 #4230061 KC 1 0.0000 mature KC10 #4227304 KC 1 1291.2036 mature KC42 #8066542 KC 1 252.6335 mature KC16 #4415241 KC 2 1822.2952 mature KC100 #11813287 KC 2 1031.6460 mature

head(wg.L$vdf)

v type claw dist age

Thermo KC B_left - mbi2 - unknown #7187384 KC 3 0.0000 mature KC no pair #4412036 KC 1 3616.7576 mature KC65;_42a left #5937084 KC 1 1691.4363 mature KC42 #11725803 KC 1 1921.1573 mature LON KC left #8262372 KC 3 2398.7528 mature KC13 #14898816 KC 1 970.6179 mature

# Alter graphs
A.R <- wg.R$g[]; dim(A.R)

# [1] 213 213

A.L <- wg.L$g[]; dim(A.L)

# [1] 209 209

sum(diag(A.R)); diag(A.R) <- 0

# [1] 0

sum(diag(A.L)); diag(A.L) <- 0

# [1] 0

g.R <- graph.adjacency(A.R, weighted=TRUE); summary(g.R)

# IGRAPH 4740778 DNW- 213 7536 -- 
# + attr: name (v/c), weight (e/n)

g.L <- graph.adjacency(A.L, weighted=TRUE); summary(g.L)

# IGRAPH ea47767 DNW- 209 9045 -- 
# + attr: name (v/c), weight (e/n)

PTR

W.R <- E(g.R)$weight
E(g.R)$weight <- rank(W.R)*2 / (ecount(g.R)+1)
summary(E(g.R)$weight)

  Min.     1st Qu.      Median   Mean    3rd Qu.       Max.

0.3578347 0.3578347 0.9181372 1 1.474194 1.999735

W.L <- E(g.L)$weight
E(g.L)$weight <- rank(W.L)*2 / (ecount(g.L)+1)
summary(E(g.L)$weight)

 Min.    1st Qu.     Median   Mean    3rd Qu.       Max.

0.299801 0.299801 1.045324 1 1.508733 1.999779

ASE

is.connected(g.R)

# [1] TRUE

is.connected(g.L)

# [1] TRUE

dmax <- 20
ase.R <- embed_adjacency_matrix(g.R, dmax)
ase.L <- embed_adjacency_matrix(g.L, dmax)
(elbow.R <- getElbows(ase.R$D, main="scree, Right"))

# [1] 1 3 9

(elbow.L <- getElbows(ase.L$D, main="scree, Left"))

# [1] 1 4 7

dhat.R <- elbow.R[2]
Xhat.R <- cbind(ase.R$X[,1:dhat.R], ase.R$Y[,1:dhat.R])
dhat.L <- elbow.L[2]
Xhat.L <- cbind(ase.L$X[,1:dhat.L], ase.L$Y[,1:dhat.L])

GMM

library(mclust)

Kmax <- 10
mc.R <- Mclust(Xhat.R, 2:Kmax, verbose = FALSE)
mc.L <- Mclust(Xhat.L, 2:Kmax, verbose = FALSE)

plot(mc.R, "BIC")

plot(mc.L, "BIC")

table(wg.R$vdf$type, mc.R$class)

/ 1 2 3 4 5 6 7

KC 26 45 14 12 0 0 3 MBIN 0 0 3 0 2 16 0 MBON 0 0 1 0 28 0 0 PN 0 0 0 0 0 0 63

adjustedRandIndex(wg.R$vdf$type, mc.R$class)

# [1] 0.5641981

table(wg.L$vdf$type, mc.L$class)

/ 1 2 3 4 5 6 7

KC 28 47 11 13 0 0 2 MBIN 0 0 0 0 21 0 0 MBON 0 0 0 0 10 19 0 PN 0 0 0 0 0 0 58

adjustedRandIndex(wg.L$vdf$type, mc.L$class)

# [1] 0.5393392

youngser/mbstructure documentation built on May 20, 2019, 2:09 p.m.