Prepare for CRAN submission

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: langevitour
 Title: Langevin Tour
-Version: 0.0.1
+Version: 0.1
 Authors@R: 
     person("Paul", "Harrison", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-3980-268X"))

NEWS.md

@@ -0,0 +1,3 @@
+# langevitour 0.1
+
+* Ready for CRAN submission.

_pkgdown.yml

@@ -1,3 +1,11 @@
 url: https://logarithmic.net/langevitour/
 template:
   bootstrap: 5
+articles:
+- title: Examples
+  navbar: ~
+  contents:
+  - usage
+  - examples
+  - rnaseq
+

vignettes/examples.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "langevitour examples"
+title: "Further examples"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{langevitour examples}
+  %\VignetteIndexEntry{Further examples}
   %\VignetteEncoding{UTF-8}
   %\VignetteEngine{knitr::rmarkdown}
 editor_options: 
@@ -20,34 +20,10 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r install, eval=FALSE}
-remotes::install_github("pfh/langevitour")
-```
-
 ```{r setup}
 library(langevitour)
 ```
 
-Things to try:
-
-* Drag labels onto the plot.
-* Set point repulsion to "local".
-* Experiment with "damping" and "heat".
-
-## Palmer Station Penguins
-
-Measurements of penguins. Since the measurements are in different units, we supply an appropriate scaling.
-
-```{r}
-library(palmerpenguins)
-
-completePenguins <- na.omit(penguins[,c(1,3,4,5,6)])
-scale <- apply(completePenguins[,-1], 2, sd)*4
-
-langevitour(completePenguins[,-1], completePenguins$species, scale=scale, pointSize=2)
-```
-
-
 ## Mouse brain cells
 
 Single-cell RNA-Seq gene expression of 2,816 mouse brain cells ([Zeisel, 2015](https://pubmed.ncbi.nlm.nih.gov/25700174/)). The top 10 principal components were produced using the steps in the [Bioconductor OSCA workflow](http://bioconductor.org/books/3.13/OSCA.workflows/zeisel-mouse-brain-strt-seq.html). This is unscaled PCA of log$_2$(normalized_count+1) expression levels, mean UMI count 15,550 per cell. So $x$ units of distance can be explained for example by $n$ genes with $x/\sqrt{n}$ log$_2$ fold change each.
@@ -130,6 +106,8 @@ langevitour(geozoo::torus.flat(p=4)$points)
 
 A dataset in the [liminal](https://sa-lee.github.io/liminal/) package. Each row has been scaled to a unit vector.
 
+* Try setting point repulsion to "outliers".
+
 ```{r}
 X <- as.matrix(liminal::pdfsense[,-(1:6)])
 X <- X / sqrt(rowSums(X*X))

vignettes/usage.Rmd

@@ -0,0 +1,43 @@
+---
+title: "Usage example"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Usage example}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+As an example we will use measurements of penguins made at Palmer Station, Antarctica. 
+
+Since the measurements are in different units, we supply an appropriate scaling.
+
+```{r}
+library(langevitour)
+library(palmerpenguins)
+
+completePenguins <- na.omit(penguins[,c(1,3,4,5,6)])
+completePenguins
+
+scale <- apply(completePenguins[,-1], 2, sd)*4
+
+langevitour(completePenguins[,-1], completePenguins$species, scale=scale, pointSize=2)
+```
+
+<br>
+
+Things to try:
+
+* Drag labels onto the plot.
+* Set point repulsion to "PCA".
+* Experiment with "damping" and "heat".
+* Hide measurements by unchecking the checkbox on their label.
+
+
+