set approx to TRUE by default

PLN-team · Mar 26, 2024 · 2744eb1 · 2744eb1
1 parent 0df94b9
commit 2744eb1
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Showing 3 changed files with 33 additions and 3 deletions.
diff --git a/R/ZIPLN.R b/R/ZIPLN.R
@@ -111,7 +111,7 @@ ZIPLN_param <- function(
   config_opt$trace <- trace
   config_opt$ftol_out  <- 1e-6
   config_opt$maxit_out <- 100
-  config_opt$approx_ZI <- FALSE
+  config_opt$approx_ZI <- TRUE
   config_opt[names(config_optim)] <- config_optim
 
   structure(list(

diff --git a/R/ZIPLNnetwork.R b/R/ZIPLNnetwork.R
@@ -86,8 +86,8 @@ ZIPLNnetwork_param <- function(
   config_opt <- config_default_nlopt
   config_opt$trace <- trace
   config_opt$ftol_out  <- 1e-6
-  config_opt$maxit_out <- 100
-  config_opt$approx_ZI <- FALSE
+  config_opt$maxit_out <- 50
+  config_opt$approx_ZI <- TRUE
   config_opt[names(config_optim)] <- config_optim
   inception_cov <- match.arg(inception_cov)
 

diff --git a/inst/case_studies/scRNA.R b/inst/case_studies/scRNA.R
@@ -8,6 +8,36 @@ scRNA$counts <- scRNA$counts[, 1:200]
 myZIPLN <- ZIPLN(counts ~ 1 + offset(log(total_counts)), zi = "col", data = scRNA)
 myPLN   <- PLN(counts ~ 1 + offset(log(total_counts)), data = scRNA)
 
+true_zeros <- scRNA$counts == 0
+n_zeros <- sum(true_zeros)
+n_nzeros <- sum(!true_zeros)
+
+data.frame(
+    fitted   = c(as.vector(fitted(myPLN)[true_zeros]), as.vector(fitted(myZIPLN)[true_zeros])),
+    obs      = rep(1:n_zeros, 2),
+    method   = factor(rep(c("PLN", "ZI (1 par per species)"), each = n_zeros))
+  ) %>%
+  ggplot() +
+  geom_rug(aes(x = fitted, color = method)) +
+  geom_point(aes(x = obs, y = fitted, color = method), size = 0.3, alpha = 0.1) +
+  ggtitle("Distribution of observed zeros as fitted by the models") +
+  xlab(label = "observations #") +
+  scale_color_viridis_d() + theme_bw()
+
+# distribution of non zero
+data.frame(
+  fitted   = c(as.vector(fitted(myPLN)[!true_zeros]), as.vector(fitted(myZIPLN)[!true_zeros])),
+  observed = rep(c(scRNA$counts[!true_zeros]), 2),
+  method   = factor(rep(c("PLN", "ZI (1 par per species)"), each = n_nzeros))
+) %>%
+  ggplot(aes(x = observed, y = fitted)) +
+  geom_point(size = .5, alpha =.25 ) +
+  facet_wrap( ~ method) +
+  scale_x_log10() +
+  scale_y_log10() +
+  theme_bw() + annotation_logticks()
+
+
 data.frame(
   fitted   = c(as.vector(fitted(myZIPLN)), as.vector(fitted(myPLN))),
   observed = rep(as.vector(scRNA$counts), 2),