Suppress messages for theta=Inf genes

saketkc · saketkc · commit 79de2753845a · 2023-10-18T19:56:46.000-04:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: sctransform
 Type: Package
 Title: Variance Stabilizing Transformations for Single Cell UMI Data
-Version: 0.4.0.9002
+Version: 0.4.0.9003
 Date: 2023-10-18
 Authors@R: c(
   person(given = "Christoph", family = "Hafemeister", email = "christoph.hafemeister@nyu.edu", role = "aut", comment = c(ORCID = "0000-0001-6365-8254")),
diff --git a/R/vst.R b/R/vst.R
@@ -935,7 +935,7 @@ reg_model_pars <- function(model_pars, genes_log_gmean_step1, genes_log_gmean, c
   all_genes <- rownames(model_pars_fit)
   # browser()
   if (exclude_poisson){
-    if (verbosity > 0) {
+    if (verbosity > 1) {
       message(paste('Replacing fit params for', length(all_poisson_genes),  'poisson genes by theta=Inf'))
     }
     for (col in intersect(colnames(x = model_pars_fit), colnames(x = vst_out_offset)) ){

Original file line number	Diff line number	Diff line change
`@@ -935,7 +935,7 @@ reg_model_pars <- function(model_pars, genes_log_gmean_step1, genes_log_gmean, c`
`935`	`935`	`all_genes <- rownames(model_pars_fit)`
`936`	`936`	`# browser()`
`937`	`937`	`if (exclude_poisson){`
`938`		`- if (verbosity > 0) {`
	`938`	`+ if (verbosity > 1) {`
`939`	`939`	`message(paste('Replacing fit params for', length(all_poisson_genes), 'poisson genes by theta=Inf'))`
`940`	`940`	`}`
`941`	`941`	`for (col in intersect(colnames(x = model_pars_fit), colnames(x = vst_out_offset)) ){`