decrease vignette size

ctlab · Oct 15, 2023 · 0e4fdf6 · 0e4fdf6
1 parent b59259c
commit 0e4fdf6
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Showing 2 changed files with 5 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: gatom
 Title: Finding an Active Metabolic Module in Atom Transition Network
-Version: 0.99.2
+Version: 0.99.3
 Authors@R: 
     c(
     person("Anastasiia", "Gainullina", role = c("aut")),

diff --git a/vignettes/gatom-tutorial.Rmd b/vignettes/gatom-tutorial.Rmd
@@ -176,22 +176,18 @@ saveModuleToHtml(module = m, file = file.path(tempdir(), "M0.vs.M1.html"),
                  name="M0.vs.M1")
 ```
 
-```{r message=FALSE, warning=FALSE}
-htmltools::includeHTML(file.path(tempdir(), "M0.vs.M1.html"))
-```
-
-
 We can also save the module to dot format:
 
 ```{r}
-saveModuleToDot(m, file = paste0(tempdir(), "M0.vs.M1.dot"), name = "M0.vs.M1")
+saveModuleToDot(m, file = file.path(tempdir(), "M0.vs.M1.dot"), name = "M0.vs.M1")
 ```
 
 Such dot file can be further used to generate svg file using `neato` tool 
 from graphviz suite if it is installed on the system:
 
 ```{r eval=FALSE}
-system(paste0("neato -Tsvg ", tempdir(), "M0.vs.M1.dot > ", tempdir(), "M0.vs.M1.svg"), 
+system(paste0("neato -Tsvg ", file.path(tempdir(), "M0.vs.M1.dot"),
+              " > ", file.path(tempdir(), "M0.vs.M1.svg")), 
        ignore.stderr=TRUE)
 ```
 
@@ -205,7 +201,7 @@ You may also set different seed for different variants of edge layout with `set.
 
 ```{r results="hide", message=FALSE, warning=FALSE}
 set.seed(42)
-saveModuleToPdf(m, file = paste0(tempdir(), "M0.vs.M1.pdf"), name = "M0.vs.M1", 
+saveModuleToPdf(m, file = file.path(tempdir(), "M0.vs.M1.pdf"), name = "M0.vs.M1", 
                 n_iter=100, force=1e-5)
 ```