fix vignette

caravagnalab · Aug 23, 2024 · 193c9cd · 193c9cd
1 parent b637109
commit 193c9cd
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Showing 8 changed files with 5 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -46,7 +46,8 @@ Imports:
     scales,
     quadprog,
     progress,
-    ggh4x
+    ggh4x,
+    Polychrome
 RoxygenNote: 7.3.1
 URL: https://github.com/caravagnalab/bascule,
     https://caravagnalab.github.io/bascule/

diff --git a/R/getters.R b/R/getters.R
@@ -86,9 +86,6 @@ get_signatures_aux = function(x, what, types=get_types(x), matrix=FALSE) {
 #'
 #' @return list of long or wide-formatted mutations counts.
 #' @export
-#'
-#' @examples
-#' get_input(example_fit)
 get_input = function(x, types=get_types(x), samples=get_samples(x),
                      clusters=get_cluster_labels(x), matrix=FALSE,
                      reconstructed=FALSE, add_groups=FALSE, by_sigs=FALSE) {

diff --git a/R/plot_exposures.R b/R/plot_exposures.R
@@ -13,9 +13,6 @@
 #'
 #' @return ggplot object.
 #' @export
-#'
-#' @examples
-#' plot_exposures(example_fit)
 plot_exposures = function(x,
                           types=get_types(x),
                           samples=get_samples(x),

diff --git a/R/plot_signatures.R b/R/plot_signatures.R
@@ -8,9 +8,6 @@
 #'
 #' @return ggplot object.
 #' @export
-#'
-#' @examples
-#' plot_signatures(example_fit)
 plot_signatures = function(x, types=get_types(x), context=T, cls=NULL,
                            signames=get_signames(x)) {
 

diff --git a/man/get_input.Rd b/man/get_input.Rd
diff --git a/man/plot_exposures.Rd b/man/plot_exposures.Rd
diff --git a/man/plot_signatures.Rd b/man/plot_signatures.Rd
diff --git a/vignettes/articles/Inference.Rmd b/vignettes/articles/Inference.Rmd
@@ -12,11 +12,10 @@ knitr::opts_chunk$set(
 ```{r setup, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(warning = FALSE, message = FALSE)
 library(bascule)
+reticulate::install_python(version="3.9.16")
 reticulate::py_install(packages="pybascule", 
-                       envname="r-reticulate", 
-                       pip=TRUE, 
+                       pip=TRUE,
                        python_version="3.9.16")
-reticulate::use_condaenv(condaenv="r-reticulate")
 py = reticulate::import("pybascule")
 ```
 
@@ -48,7 +47,7 @@ K_list = 0:7
 
 Now, we can fit the model. Let's first fit the NMF to perform signatures deconvolution. 
 ```{r}
-x = fit(counts=counts, k_list=K_list, n_steps=3000,
+x = fit(counts=counts, k_list=K_list, n_steps=300,
         reference_cat=reference_cat,
         keep_sigs=c("SBS1","SBS5"), # force fixed signatures
         store_fits=TRUE, py=py)