diff --git a/DESCRIPTION b/DESCRIPTION index 0b323b10..7deb21a4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: microViz Title: Microbiome Data Analysis and Visualization -Version: 0.8.0.9005 +Version: 0.8.0.9006 Authors@R: person(given = "David", family = "Barnett", diff --git a/R/ord_explore.R b/R/ord_explore.R index c34936ae..1e3f0ef9 100644 --- a/R/ord_explore.R +++ b/R/ord_explore.R @@ -628,7 +628,9 @@ ord_explore <- function(data, eventExpr = input$trans, handlerExpr = { x <- dist_choices(init$data, type = "all") - if (input$trans %in% trans_choices("log")) x <- x[x != "aitchison"] + if (input$trans %in% trans_choices("log")) { + x <- x[!x %in% c("aitchison", "jsd")] + } shiny::updateSelectizeInput( session = session, inputId = "dist", choices = x ) @@ -1136,11 +1138,10 @@ dist_choices <- function(data, type) { "va-wunifrac" = "va-wunifrac: variance-adjusted weighted UniFrac" ) # add more phyloseq dist methods - pdists <- c( - phyloseq::distanceMethodList$vegdist, - phyloseq::distanceMethodList$betadiver, - phyloseq::distanceMethodList$DPCoA - ) + pdists <- unlist(c( + "maximum", "binary", + phyloseq::distanceMethodList[c("vegdist", "betadiver", "DPCoA")] + )) more <- stats::setNames(object = pdists, nm = pdists) all <- c(all, more[!names(more) %in% names(all)]) diff --git a/tests/testthat/_snaps/ord_explore.md b/tests/testthat/_snaps/ord_explore.md index 9639f6d3..83120ca6 100644 --- a/tests/testthat/_snaps/ord_explore.md +++ b/tests/testthat/_snaps/ord_explore.md @@ -222,16 +222,16 @@ Code dist_choices(esophagus, type = "tree") Output - gunifrac (Generalised UniFrac, alpha=0.5) - "gunifrac" - wunifrac (weighted UniFrac) - "wunifrac" - unifrac (unweighted UniFrac) - "unifrac" - va-wunifrac (variance adjusted weighted) - "va-wunifrac" - dpcoa - "dpcoa" + gunifrac: Generalised UniFrac, alpha=0.5 + "gunifrac" + wunifrac: weighted UniFrac + "wunifrac" + unifrac: unweighted UniFrac + "unifrac" + va-wunifrac: variance-adjusted weighted UniFrac + "va-wunifrac" + dpcoa + "dpcoa" # ord_choices helper works diff --git a/tests/testthat/_snaps/ord_explore/dietDistsAll.csv b/tests/testthat/_snaps/ord_explore/dietDistsAll.csv index 8fa52c90..9b292001 100644 --- a/tests/testthat/_snaps/ord_explore/dietDistsAll.csv +++ b/tests/testthat/_snaps/ord_explore/dietDistsAll.csv @@ -1,9 +1,11 @@ "","x" -"none (for PCA/RDA/CCA)","none" -"bray (Bray-Curtis)","bray" -"aitchison (a.k.a. CLR & euclidean)","aitchison" +"none: no distance used for PCA/RDA/CCA","none" +"bray: Bray-Curtis","bray" +"aitchison: CLR & Euclidean","aitchison" "euclidean","euclidean" -"jsd","jsd" +"jsd: Jensen-Shannon Divergence","jsd" +"maximum","maximum" +"binary","binary" "manhattan","manhattan" "canberra","canberra" "kulczynski","kulczynski" @@ -41,7 +43,3 @@ "sim","sim" "gl","gl" "z","z" -"maximum","maximum" -"binary","binary" -"minkowski","minkowski" -"ANY","ANY" diff --git a/tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv b/tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv index 8fa52c90..9b292001 100644 --- a/tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv +++ b/tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv @@ -1,9 +1,11 @@ "","x" -"none (for PCA/RDA/CCA)","none" -"bray (Bray-Curtis)","bray" -"aitchison (a.k.a. CLR & euclidean)","aitchison" +"none: no distance used for PCA/RDA/CCA","none" +"bray: Bray-Curtis","bray" +"aitchison: CLR & Euclidean","aitchison" "euclidean","euclidean" -"jsd","jsd" +"jsd: Jensen-Shannon Divergence","jsd" +"maximum","maximum" +"binary","binary" "manhattan","manhattan" "canberra","canberra" "kulczynski","kulczynski" @@ -41,7 +43,3 @@ "sim","sim" "gl","gl" "z","z" -"maximum","maximum" -"binary","binary" -"minkowski","minkowski" -"ANY","ANY" diff --git a/tests/testthat/_snaps/ord_explore/esoDistsAll.csv b/tests/testthat/_snaps/ord_explore/esoDistsAll.csv index 2994d3fa..df6e12c3 100644 --- a/tests/testthat/_snaps/ord_explore/esoDistsAll.csv +++ b/tests/testthat/_snaps/ord_explore/esoDistsAll.csv @@ -1,14 +1,15 @@ "","x" -"none (for PCA/RDA/CCA)","none" -"bray (Bray-Curtis)","bray" -"aitchison (a.k.a. CLR & euclidean)","aitchison" +"none: no distance used for PCA/RDA/CCA","none" +"bray: Bray-Curtis","bray" +"aitchison: CLR & Euclidean","aitchison" "euclidean","euclidean" -"gunifrac (Generalised UniFrac, alpha=0.5)","gunifrac" -"unifrac (unweighted UniFrac)","unifrac" -"wunifrac (weighted UniFrac)","wunifrac" -"va-wunifrac (variance adjusted weighted)","va-wunifrac" -"dpcoa","dpcoa" -"jsd","jsd" +"jsd: Jensen-Shannon Divergence","jsd" +"gunifrac: Generalised UniFrac, alpha=0.5","gunifrac" +"unifrac: unweighted UniFrac","unifrac" +"wunifrac: weighted UniFrac","wunifrac" +"va-wunifrac: variance-adjusted weighted UniFrac","va-wunifrac" +"maximum","maximum" +"binary","binary" "manhattan","manhattan" "canberra","canberra" "kulczynski","kulczynski" @@ -46,7 +47,4 @@ "sim","sim" "gl","gl" "z","z" -"maximum","maximum" -"binary","binary" -"minkowski","minkowski" -"ANY","ANY" +"dpcoa","dpcoa" diff --git a/tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv b/tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv index 8fa52c90..9b292001 100644 --- a/tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv +++ b/tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv @@ -1,9 +1,11 @@ "","x" -"none (for PCA/RDA/CCA)","none" -"bray (Bray-Curtis)","bray" -"aitchison (a.k.a. CLR & euclidean)","aitchison" +"none: no distance used for PCA/RDA/CCA","none" +"bray: Bray-Curtis","bray" +"aitchison: CLR & Euclidean","aitchison" "euclidean","euclidean" -"jsd","jsd" +"jsd: Jensen-Shannon Divergence","jsd" +"maximum","maximum" +"binary","binary" "manhattan","manhattan" "canberra","canberra" "kulczynski","kulczynski" @@ -41,7 +43,3 @@ "sim","sim" "gl","gl" "z","z" -"maximum","maximum" -"binary","binary" -"minkowski","minkowski" -"ANY","ANY"