Update vignettes

keyes-timothy · Aug 25, 2024 · cd770dc · cd770dc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidytof
 Title: Analyze High-dimensional Cytometry Data Using Tidy Data Principles
-Version: 0.99.7
+Version: 0.99.8
 Authors@R: 
     c(person(given = "Timothy",
              family = "Keyes",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# tidytof 0.99.8
+
+NEW FEATURES
+
+* Vignette bug fixes. 
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* None
+
 # tidytof 0.99.7
 
 NEW FEATURES

diff --git a/vignettes/clustering.Rmd b/vignettes/clustering.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how to identify clusters of cells with shared
   phenotypic characteristics using {tidytof}.
 vignette: >
-  %\VignetteIndexEntry{Clustering and metaclustering}
+  %\VignetteIndexEntry{07. Clustering and metaclustering}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/contributing-to-tidytof.Rmd b/vignettes/contributing-to-tidytof.Rmd
@@ -4,7 +4,7 @@ output: rmarkdown::html_vignette
 description: > 
   Read this vignette to learn how to contribute code of your own to {tidytof}.
 vignette: >
-  %\VignetteIndexEntry{How to contribute code}
+  %\VignetteIndexEntry{11. How to contribute code}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/differential-discovery-analysis.Rmd b/vignettes/differential-discovery-analysis.Rmd
@@ -8,7 +8,7 @@ description: >
   expression across experimental/clinical variables using various statistical
   tools.
 vignette: >
-  %\VignetteIndexEntry{Differential discovery analysis}
+  %\VignetteIndexEntry{08. Differential discovery analysis}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/dimensionality-reduction.Rmd b/vignettes/dimensionality-reduction.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how visualize single-cell phenotypes in 
   low-dimensional space using dimensionality reduction algorithms (PCA, UMAP, tSNE)
 vignette: >
-  %\VignetteIndexEntry{Dimensionality reduction}
+  %\VignetteIndexEntry{06. Dimensionality reduction}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/downsampling.Rmd b/vignettes/downsampling.Rmd
@@ -8,7 +8,7 @@ description: >
   dataset to a smaller 
   number of cells using {tidytof}.
 vignette: >
-  %\VignetteIndexEntry{Downsampling}
+  %\VignetteIndexEntry{05. Downsampling}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/feature-extraction.Rmd b/vignettes/feature-extraction.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how to compute summary statistics like cluster 
   abundance and cluster marker expression using {tidytof} 
 vignette: >
-  %\VignetteIndexEntry{Feature extraction}
+  %\VignetteIndexEntry{09. Feature extraction}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/modeling.Rmd b/vignettes/modeling.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how to compute summary statistics like cluster 
   abundance and cluster marker expression using {tidytof} 
 vignette: >
-  %\VignetteIndexEntry{Modeling}
+  %\VignetteIndexEntry{10. Modeling}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/preprocessing.Rmd b/vignettes/preprocessing.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how to clean and preprocess CyTOF data using 
   {tidytof}.
 vignette: >
-  %\VignetteIndexEntry{Preprocessing}
+  %\VignetteIndexEntry{04. Preprocessing}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/quality-control.Rmd b/vignettes/quality-control.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how to perform basic quality control analyses on 
   high-dimensional cytometry data with {tidytof}. 
 vignette: >
-  %\VignetteIndexEntry{Quality control}
+  %\VignetteIndexEntry{03. Quality control}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/reading-and-writing-data.Rmd b/vignettes/reading-and-writing-data.Rmd
@@ -7,7 +7,7 @@ description: >
   Read this vignette to learn how to read data from FCS and CSV files
   on disk and how to write data to FCS and CSV files on disk. 
 vignette: >
-  %\VignetteIndexEntry{Reading and writing data}
+  %\VignetteIndexEntry{02. Reading and writing data}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/tidytof.Rmd b/vignettes/tidytof.Rmd
@@ -9,7 +9,7 @@ description: >
   learn about tidytof's basic design schema, its main capabilities, 
   and where to find more information. 
 vignette: >
-  %\VignetteIndexEntry{Getting started with tidytof}
+  %\VignetteIndexEntry{01. Getting started with tidytof}
   %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---
@@ -171,11 +171,17 @@ Finally, it means that `{tidytof}` is optimized first for ease-of-use, then for
 
 # Where to go next
 
-`{tidytof}` includes multiple vignettes that cover different components of the prototypical high-dimensional cytometry data analysis pipeline. To learn the basics, we recommend visiting the vignettes in the following order to start with smalle (cell-level) operations and work your way up to larger (cluster- and sample-level) operations: 
+`{tidytof}` includes multiple vignettes that cover different components of the prototypical high-dimensional cytometry data analysis pipeline. You can access these vignettes by running the following: 
+
+```{r, eval = FALSE}
+browseVignettes(package = "tidytof")
+```
+
+To learn the basics, we recommend visiting the vignettes in the following order to start with smalle (cell-level) operations and work your way up to larger (cluster- and sample-level) operations: 
 
 * Reading and writing data
-* Preprocessing
 * Quality control
+* Preprocessing
 * Downsampling
 * Dimensionality reduction
 * Clustering and metaclustering