Merge branch 'main' into gh-pages

Author: mvfki

.Rbuildignore

@@ -8,3 +8,5 @@
 ^docs$
 ^pkgdown$
 ^vignettes/rotating_tetra\.gif$
+\.h5ad$
+\.loom$

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: CytoSimplex
 Type: Package
 Title: Simplex Visualization of Cell Fate Similarity in Single-Cell Data
-Version: 0.1.99
+Version: 0.2.0
+Date: 2025-04-22
 Authors@R: c(
     person(given = 'Yichen', family = 'Wang', email = 'wayichen@umich.edu', 
            role = c('aut', 'cre'), comment = c(ORCID = "0000-0003-4347-5199")),
@@ -14,7 +15,7 @@ Maintainer: Yichen Wang <wayichen@umich.edu>
 Description: Create simplex plots to visualize the similarity between 
     single-cells and selected clusters in a 1-/2-/3-simplex space.
     Velocity information can be added as an additional layer. 
-    See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.
+    See Liu J, Wang Y et al (2023) <doi:10.1093/bioinformatics/btaf119> for more details.
 URL: https://welch-lab.github.io/CytoSimplex/, https://github.com/welch-lab/CytoSimplex
 License: GPL-3
 Encoding: UTF-8
@@ -47,6 +48,6 @@ Suggests:
     SingleCellExperiment,
     SummarizedExperiment,
     testthat (>= 3.0.0)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 VignetteBuilder: knitr

R/quaternary.R

@@ -174,14 +174,16 @@ plotQuaternary.default <- function(
         return(plotQuaternary(x = simMat, veloMat = veloMat,
                colorArg = colorArg, ...))
     } else {
+        # If specified in `...`, use that. Otherwise, always assume the default
+        # to be `TRUE`. Note an instance of this parameter does not exist yet,
+        # thus created.
         interactive <- list(...)$interactive %||% TRUE
         if (isTRUE(interactive)) {
             cli::cli_alert_warning(
                 "Interactive view with {.pkg plotly} can show desired cluster(s) by clicking on the legend. Ignoring {.var byCluster}."
             )
             return(plotQuaternary(
-                x = simMat, veloMat = veloMat, colorArg = colorArg,
-                interactove = TRUE, ...
+                x = simMat, veloMat = veloMat, colorArg = colorArg, ...
             ))
         }
         if (identical(byCluster, "all")) {

README.md

@@ -32,6 +32,6 @@ We have created a [documentation website](https://welch-lab.github.io/CytoSimple
 
 ## Citation
 
-If you used CytoSimplex in your work, please cite the following work:
+If you used CytoSimplex in your work, please cite the following work published on *Bioinformatics*:
 
->[Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono and Joshua D. Welch, CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex, 2023, bioRxiv](https://doi.org/10.1101/2023.12.07.570655)
+>Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono and Joshua D. Welch, CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex, 2025, *Bioinformatics*, [(https://doi.org/10.1093/bioinformatics/btaf119)](https://doi.org/10.1093/bioinformatics/btaf119)

tests/testthat/test-quaternary.R

@@ -43,6 +43,9 @@ test_that("Test quaternary - sparse", {
     expect_no_error(plotQuaternary(rnaRaw, rnaCluster, vertices, gene,
                                    veloGraph = rnaVelo, interactive = TRUE,
                                    title = "All cells"))
+    expect_message(plotQuaternary(rnaRaw, rnaCluster, vertices, gene, byCluster = TRUE,
+                                  interactive = TRUE),
+                   "can show desired cluster\\(s\\) by clicking on the legend")
 })
 
 test_that("Test quaternary - dense", {