page update

CostaLab · Oct 17, 2024 · 276337e · 276337e
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commit 276337e
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Showing 8 changed files with 20 additions and 19 deletions.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -27,3 +27,6 @@ navbar:
      install:
       text: Install
       href: articles/Install.html
+  url:
+    reference: https://github.com/CostaLab/CrossTalkeR/reference
+    article: https://github.com/CostaLab/CrossTalkeR/articles
diff --git a/docs/articles/CrossTalkeR.html b/docs/articles/CrossTalkeR.html
diff --git a/docs/articles/HumanFibrosis.html b/docs/articles/HumanFibrosis.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -9,4 +9,4 @@ articles:
   LR2TF_analysis: LR2TF_analysis.html
   MyocardialInfarction: MyocardialInfarction.html
   run_liana: run_liana.html
-last_built: 2024-10-16T14:02Z
+last_built: 2024-10-17T07:40Z
diff --git a/docs/search.json b/docs/search.json
diff --git a/vignettes/CrossTalkeR.Rmd b/vignettes/CrossTalkeR.Rmd
@@ -45,17 +45,16 @@ In our vignette we provide examples on how to analyse cell interactions from a h
 
 
 ```{r vignete1, results="hide", warning=FALSE,message=F, output=FALSE, eval = FALSE}
-paths <- c('CTR' = system.file("extdata",
-                               "CTR_LR.csv",
-                               package = "CrossTalkeR"),
-           'EXP' = system.file("extdata",
-                               "EXP_LR.csv",
-                               package = "CrossTalkeR"))
+data(CTR)
+data(EXP)
+paths <- list('CTR'=CTR,
+              'EXP'=EXP)
+
 genes <- c('TGFB1|L')
 output <- system.file("extdata", package = "CrossTalkeR")
 data <- generate_report(paths,
                         genes,
-                        out_path=paste0(output,'/'),
+                        out_path=file.path(output),
                         threshold=0,
                         out_file = 'vignettes_example.html',
                         output_fmt = "html_document",

diff --git a/vignettes/CrossTalker_basicusage.rmd b/vignettes/CrossTalker_basicusage.rmd
@@ -44,7 +44,7 @@ author:
 output:
      html_document
 vignette: |
-      %\VignetteIndexEntry{CrossTalkeR-install-basicusage}
+      %\VignetteIndexEntry{CrossTalkeR-basicusage}
       %\VignetteEngine{knitr::rmarkdown}
       %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/HumanFibrosis.rmd b/vignettes/HumanFibrosis.rmd
@@ -110,7 +110,7 @@ paths <- list('CTR'=CTR,
 
 output <- system.file("extdata", package = "CrossTalkeR")
 ctkroutput <- generate_report(paths,
-                out_path=paste0(output,'/'),
+                out_path=file.path(output),
                 out_file = 'vignettes_example.html',
                 output_fmt = "html_document",
                 report = FALSE,