Merge branch 'main' into gh-pages

R/quaternary.R

@@ -8,7 +8,7 @@
 #' A dynamic rotating view in a GIF image file can be created with
 #' \code{\link{writeQuaternaryGIF}}. Package \code{magick} must be installed in
 #' advance. Linux users may refer to this
-#' \href{https://cran.r-project.org/web/packages/magick/vignettes/intro.html#Build_from_source}{installation guide}.
+#' \href{https://cran.r-project.org/package=magick/vignettes/intro.html#Build_from_source}{installation guide}.
 #' @param x Input data. Can be a \code{matrix} or \code{dgCMatrix} object with
 #' cells as columns, a \code{Seurat} or \code{SingleCellExperiment} object.
 #' "simMat" method takes intermediate values.

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://codecov.io/gh/mvfki/CytoSimplex)[![Seurat](https://img.shields.io/badge/Seurat-5.0.1-blue)](https://cran.r-project.org/web/packages/Seurat/index.html)[![sce](https://img.shields.io/badge/SingleCellExperiment-1.22.0-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/mvfki/CytoSimplex/branch/main/graph/badge.svg?token=AYU2AOE25I)](https://app.codecov.io/gh/mvfki/CytoSimplex)[![Seurat](https://img.shields.io/badge/Seurat-5.0.1-blue)](https://CRAN.R-project.org/package=Seurat)[![sce](https://img.shields.io/badge/SingleCellExperiment-1.22.0-blue)](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
 
 
 CytoSimplex is an R package that creates simplex plot showing similarity between single-cells and terminals represented by clusters of cells. RNA velocity can be added as another layer of information.
@@ -23,5 +23,5 @@ We will submit the package to CRAN soon to simplify the installation process.
 
 ## Tutorial
 
-We have created a [documentation website](https://welch-lab.github.io/CytoSimplex) for posting [example tutorials](https://welch-lab.github.io/CytoSimplex/articles/CytoSimplex.html) walking through the process from loading the provided example data and creating different types of visualization.
+We have created a [documentation website](https://welch-lab.github.io/CytoSimplex/) for posting [example tutorials](https://welch-lab.github.io/CytoSimplex/articles/CytoSimplex.html) walking through the process from loading the provided example data and creating different types of visualization.
 

vignettes/CytoSimplex.Rmd

@@ -125,7 +125,7 @@ plotQuaternary(rnaRaw, clusterVar = rnaCluster, vertices = vt.quat,
 
 **↑↑↑Try drag it!**
 
-We have also implemented of GIF image generator that rotates the tetrahedron rounding the z-axis. Note that package `magick` is required for this feature. (<a href="https://cran.r-project.org/web/packages/magick/vignettes/intro.html#Installing_magick" target="_blank">See here for how to install `magick` in detail</a>)
+We have also implemented of GIF image generator that rotates the tetrahedron rounding the z-axis. Note that package `magick` is required for this feature. (<a href="https://cran.r-project.org/package=magick/vignettes/intro.html#Installing_magick" target="_blank">See here for how to install `magick` in detail</a>)
 
 ```{R writeGIF, results="hide"}
 writeQuaternaryGIF(rnaRaw, clusterVar = rnaCluster, vertices = vt.quat,