mc + vignettes

caravagnalab · Aug 23, 2024 · b637109 · b637109
1 parent 28f62b3
commit b637109
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Showing 9 changed files with 12 additions and 21 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,7 +45,8 @@ Imports:
     patchwork,
     scales,
     quadprog,
-    progress
+    progress,
+    ggh4x
 RoxygenNote: 7.3.1
 URL: https://github.com/caravagnalab/bascule,
     https://caravagnalab.github.io/bascule/

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(plot,bascule_obj)
 S3method(print,bascule_obj)
 export(configure_environment)
 export(fit)
@@ -13,6 +12,7 @@ export(have_loaded_env)
 export(have_python_deps)
 export(load_conda_env)
 export(merge_clusters)
+export(plot.bascule_obj)
 export(plot_data)
 export(plot_exposures)
 export(plot_scores)

diff --git a/R/plot_mutations.R b/R/plot_mutations.R
@@ -9,9 +9,6 @@
 #'
 #' @return ggplot object.
 #' @export
-#'
-#' @examples
-#' plot_data(example_fit)
 plot_data = function(x, types=get_types(x), samples=get_samples(x),
                      clusters=get_cluster_labels(x), reconstructed=TRUE,
                      color_by_sigs=FALSE) {

diff --git a/R/print_S3.R b/R/print_S3.R
@@ -86,11 +86,8 @@ print.bascule_obj = function(x, ...)
 #'
 #' @return Nothing.
 #'
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' }
+#' @export plot.bascule_obj
+
 plot.bascule_obj = function(x, ...)
 {
   stopifnot(inherits(x, "cnaqc"))

diff --git a/data/example_dataset.rda b/data/example_dataset.rda
diff --git a/data/example_fit.rda b/data/example_fit.rda
diff --git a/man/plot.bascule_obj.Rd b/man/plot.bascule_obj.Rd
diff --git a/man/plot_data.Rd b/man/plot_data.Rd
diff --git a/vignettes/articles/Inference.Rmd b/vignettes/articles/Inference.Rmd
@@ -12,8 +12,11 @@ knitr::opts_chunk$set(
 ```{r setup, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(warning = FALSE, message = FALSE)
 library(bascule)
-configure_environment(use_default=TRUE)
-reticulate::use_condaenv(condaenv="bascule-env")
+reticulate::py_install(packages="pybascule", 
+                       envname="r-reticulate", 
+                       pip=TRUE, 
+                       python_version="3.9.16")
+reticulate::use_condaenv(condaenv="r-reticulate")
 py = reticulate::import("pybascule")
 ```
 
@@ -46,13 +49,13 @@ 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,
-        reference_cat=reference_cat, 
+        reference_cat=reference_cat,
         keep_sigs=c("SBS1","SBS5"), # force fixed signatures
         store_fits=TRUE, py=py)
 ```
 
 ```{r}
-print(x)
+x
 ```