minor tweaks to pkgdown docs

campbio · Jul 19, 2021 · 8fbd7ee · 8fbd7ee
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: celda
 Title: CEllular Latent Dirichlet Allocation
-Version: 1.9.1
+Version: 1.9.2
 Authors@R: c(person("Joshua", "Campbell", email = "[email protected]",
     role = c("aut", "cre")),
     person("Sean", "Corbett", email = "[email protected]", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,8 @@
+# celda 1.9.2
+
+* Added a `NEWS.md` file to track changes to the package.
+* Added new tutorials and documentation generated with pkgdown.
+* Removed warnings in plotRPC functions.
+* Added use of "displayName" to several functions that show feature names. 
+* Minor bug fix when the input matrix was sparse and contained non-integer values.
+* Several improvements to plotting functions. 
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/campbio/celda.svg?branch=master)](https://travis-ci.org/campbio/celda)
+[![Build Status](https://travis-ci.com/campbio/celda.svg?branch=master)](https://travis-ci.com/campbio/celda)
 [![Coverage Status](https://coveralls.io/repos/github/campbio/celda/badge.svg?branch=master)](https://coveralls.io/github/campbio/celda?branch=master)
 
 # celda: CEllular Latent Dirichlet Allocation

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -106,11 +106,13 @@ navbar:
       href: articles/articles/installation.html
     - text: "Vignettes"
       menu:
-      - text: "Analysis of PBMC3K with Celda"
+      - text: "Celda - Analysis of PBMC3K"
         href: articles/articles/celda_pbmc3k.html
-      - text: "Decontamination of PBMC4K with DecontX"
+      - text: "DecontX - Decontamination of PBMC4K"
         href: articles/articles/decontX_pbmc4k.html
     - text: "Reference"
       href: reference/index.html
+    - text: "News"
+      href: news/index.html
     - icon: fa-github
       href: https://github.com/campbio/celda
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/articles/celda_pbmc3k.html b/docs/articles/articles/celda_pbmc3k.html
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png
diff --git a/.../articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png b/.../articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png
diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png