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Add option to set mu flat

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kieranrcampbell committed Feb 14, 2019
1 parent 289b9a2 commit a5bdaeaa2d21352a398617398a4f2d496a9bd237
Showing with 13 additions and 5 deletions.
  1. +4 −2 R/clonealign.R
  2. +6 −1 R/inference-tflow.R
  3. +1 −1 man/clonealign.Rd
  4. +2 −1 man/inference_tflow.Rd
@@ -120,7 +120,8 @@ clonealign <- function(gene_expression_data,
K = NULL,
B = 20,
verbose = TRUE,
seed = NULL) {
seed = NULL,
data_init_mu = TRUE) {

N <- NA # Number of cells
G <- NA # Number of genes
@@ -187,7 +188,8 @@ clonealign <- function(gene_expression_data,
K = K,
B = B,
verbose = verbose,
seed = seed)
seed = seed,
data_init_mu = data_init_mu)


rlist <- list(
@@ -49,7 +49,8 @@ inference_tflow <- function(Y_dat,
B = 20,
mc_samples = 1,
verbose = TRUE,
seed = NULL) {
seed = NULL,
data_init_mu = data_init_mu) {

# Do a first check that we actually have tensorflow support
if(!reticulate::py_module_available("tensorflow")) {
@@ -180,6 +181,10 @@ inference_tflow <- function(Y_dat,

mu_guess <- colMeans(data$Y / rowMeans(data$Y)) / rowMeans(data$L)
mu_guess <- mu_guess[-1] / mu_guess[1]

if(!data_init_mu) {
mu_guess <- rep(1, length(mu_guess))
}


# Tensors for dispersion basis functions ----------

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