test/test_classtpx.R

In kkdey/classtpx: MAP Estimation using topic models in a semi-supervised set up where there are few samples with known topic proportions or known to belong to some cluster exclusively and there are samples for which no such information are available.

############  test classtpx   ####################

library(maptpx)
library(classtpx)
counts <- get(load("../singlecell-clustering/output/GTEX_heart.rda"))
A_est <- get(load("../singlecell-clustering/output/A.total.14.rda"))
topic_clust = classtpx::class_topics(
  t(counts),
  K = 14,
  #known_samples = A.heart.12,
  #class_labs = rep(dim(data_heart)[2],"heart"),
  optional_theta = as.matrix(A_est[,1:14]),
  method = "theta.fix",
  tol = 0.01,
  shrink = FALSE
)



method = "theta.fix"
optional_theta <- A_est
shrink=FALSE
mash_user=NULL
shape=NULL
initopics=NULL
tol=0.1
bf=FALSE
kill=2
ord=TRUE 
verb=1
tmax=10000
wtol=10^(-4)
qn=100
grp=NULL
admix=TRUE
prior_omega = NULL
trim = 0
nonzero=FALSE
dcut=-10

known_samples=NULL
class_labs=NULL
K <- dim(optional_theta)[2]