more fixes

README.md

@@ -1,6 +1,6 @@
 # CytoSimplex <img src="man/figures/logo.png" align="right" width="120" />
 
-[![R_CMD_check](https://github.com/welch-lab/CytoSimplex/actions/workflows/R_CMD_check.yml/badge.svg?branch=main)](https://github.com/welch-lab/CytoSimplex/actions/workflows/R_CMD_check.yml)[![codecov](https://codecov.io/gh/mvfki/CytoSimplex/branch/main/graph/badge.svg?token=AYU2AOE25I)](https://app.codecov.io/gh/mvfki/CytoSimplex)[![Seurat](https://img.shields.io/badge/Seurat-5.1.0-blue)](https://CRAN.R-project.org/package=Seurat)[![sce](https://img.shields.io/badge/SingleCellExperiment-1.26.0-blue)](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
+[![R_CMD_check](https://github.com/welch-lab/CytoSimplex/actions/workflows/R_CMD_check.yml/badge.svg?branch=main)](https://github.com/welch-lab/CytoSimplex/actions/workflows/R_CMD_check.yml)[![codecov](https://codecov.io/gh/welch-lab/CytoSimplex/branch/main/graph/badge.svg?token=AYU2AOE25I)](https://app.codecov.io/gh/welch-lab/CytoSimplex)[![Seurat](https://img.shields.io/badge/Seurat-5.1.0-blue)](https://CRAN.R-project.org/package=Seurat)[![sce](https://img.shields.io/badge/SingleCellExperiment-1.26.0-blue)](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
 [![PyPI version](https://badge.fury.io/py/CytoSimplex.svg)](https://badge.fury.io/py/CytoSimplex)
 
 

_pkgdown.yml

@@ -3,6 +3,18 @@ template:
   bootstrap: 5
 
 navbar:
+  title: CytoSimplex
+  left:
+    - text: Tutorials
+      menu:
+        - text: HSPC analysis
+          href: articles/HSPC_example.html
+        - text: General usage with BMSC subset
+          href: articles/CytoSimplex.html
+    - text: API
+      href: reference/index.html
+    - text: Changelog
+      href: NEWS.html
   right:
     - icon: fab fa-github fa-lg
       href: https://github.com/welch-lab/CytoSimplex

vignettes/CytoSimplex.Rmd

@@ -51,7 +51,7 @@ head(stats)
 
 `plotTernary()` shows sample similarity in a ternary simplex -- equilateral triangle. The closer a dot, a cell, is to one vertex, the more similar the cell is to the cell cluster(s) the vertex represents. We recommend that users select the top marker genes for each terminal and only use them is the features for calculating the similarity.
 
-```{R plotTernary, fig.height = 4, fig.width = 4}
+```{R plotTernary, fig.height = 4, fig.width = 5}
 vt.tern <- c("OS", "RE", "CH")
 gene.tern <- selectTopFeatures(rnaRaw, clusterVar = rnaCluster, vertices = vt.tern)
 plotTernary(rnaRaw, clusterVar = rnaCluster, vertices = vt.tern, features = gene.tern)
@@ -69,7 +69,7 @@ print(paste0("Class of `rnaVelo`: ", class(rnaVelo),
 
 We create a number of square grids in the 2D plain of the ternary simplex (or cube grids in 3D space of the quaternary simplex), and aggregate the cells fall into each grid with taking the mean of velocity towards each of the vertices. Finally, we draw an arrow from the grid center pointing to each vertex with the length representing the aggregated mean velocity. 
 
-```{R ternVelo, fig.width = 4, fig.height = 4}
+```{R ternVelo, fig.width = 5, fig.height = 4}
 plotTernary(rnaRaw, clusterVar = rnaCluster, vertices = vt.tern, 
             features = gene.tern, veloGraph = rnaVelo)
 ```
@@ -122,12 +122,7 @@ We have also implemented of GIF image generator that rotates the tetrahedron rou
 ```{R writeGIF, eval=FALSE, results="hide"}
 writeQuaternaryGIF(rnaRaw, clusterVar = rnaCluster, vertices = vt.quat, 
                    features = gene.quat, veloGraph = rnaVelo, 
-                   gifPath = "rotating_tetra.gif")
-```
-
-```{R showGIF, echo = FALSE}
-if (!knitr:::is_latex_output()) {
-  knitr::include_graphics(system.file("figure/rotating_tetra.gif", package = "CytoSimplex"))
-}
+                   width = 8, height = 5, res = 200)
 ```
 
+<img src="https://raw.githubusercontent.com/welch-lab/CytoSimplex/refs/heads/main/inst/figure/rotating_tetra.gif" width="480" style="display: block; margin: auto;"/>