fix: fixed erroneous taxon ordering that occurred if comp_barplot tax…

…_level is set to "Taxon" - as occurred in the tax_rename documentation!

https://david-barnett.github.io/microViz/reference/tax_rename.html

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: microViz
 Title: Microbiome Data Analysis and Visualization
-Version: 0.10.9
+Version: 0.10.10
 Authors@R: 
     person(given = "David",
            family = "Barnett",

NEWS.md

@@ -1,3 +1,7 @@
+# microViz 0.10.10
+
+- Fix: `comp_barplot` taxon ordering is now correct when tax_level is set to "Taxon"
+
 # microViz 0.10.9
 
 - Fix: Small internal fix to avoid renderggiraph deprecation warning in ord_explore.

R/comp_barplot.R

@@ -217,6 +217,9 @@ comp_barplot <- function(ps,
                          x = "SAMPLE",
                          ...) {
   ps <- ps_get(ps)
+  if (identical(tax_level, ".Taxon")) {
+    stop("'.Taxon' cannot be used as a rank name! You must rename that rank.")
+  }
   if (!rlang::is_scalar_integerish(n_taxa) || n_taxa < 1) {
     stop("n_taxa must a positive integer")
   }
@@ -378,7 +381,7 @@ comp_barplotFixed <- function(ps, interactive,
   df <- ps_melt(ps)
 
   # set fixed order of stacked taxa bars by creating ordered factor
-  df[["Taxon"]] <- factor(df[["unique"]], levels = rev(uniqueTaxaOrdered))
+  df[[".Taxon"]] <- factor(df[["unique"]], levels = rev(uniqueTaxaOrdered))
 
   # # set fixed order of fill colours (for LEGEND ordering!)
   df[[tax_level]] <- factor(df[[".top"]], levels = topTaxaOrdered)
@@ -390,7 +393,7 @@ comp_barplotFixed <- function(ps, interactive,
   # build plot
   p <- ggplot2::ggplot(data = df, mapping = ggplot2::aes(
     x = .data[[x]], y = .data[["Abundance"]],
-    fill = .data[[tax_level]], group = .data[["Taxon"]]
+    fill = .data[[tax_level]], group = .data[[".Taxon"]]
   ))
   if (identical(x, "SAMPLE")) p <- p + ggplot2::xlab(NULL)
 

README.Rmd

@@ -121,7 +121,7 @@ install.packages("devtools")
 devtools::install_github("david-barnett/microViz")
 
 # To install a specific "release" version of this package, e.g. an old version 
-devtools::install_github("david-barnett/[email protected].8") 
+devtools::install_github("david-barnett/[email protected].10") 
 ```
 
 ### Installation notes

README.md

@@ -133,7 +133,7 @@ install.packages("devtools")
 devtools::install_github("david-barnett/microViz")
 
 # To install a specific "release" version of this package, e.g. an old version 
-devtools::install_github("david-barnett/[email protected].8") 
+devtools::install_github("david-barnett/[email protected].10") 
 ```
 
 ### Installation notes
@@ -159,7 +159,7 @@ formally test this.
 
 ``` r
 library(microViz)
-#> microViz version 0.10.9 - Copyright (C) 2023 David Barnett
+#> microViz version 0.10.10 - Copyright (C) 2023 David Barnett
 #> ! Website: https://david-barnett.github.io/microViz
 #> ✔ Useful?  For citation details, run: `citation("microViz")`
 #> ✖ Silence? `suppressPackageStartupMessages(library(microViz))`
@@ -331,8 +331,8 @@ aitchison_perm <- aitchison_dists %>%
     n_processes = 1, n_perms = 99, # you should use at least 999!
     variables = "bmi_group"
   )
-#> 2023-05-15 21:22:34.548391 - Starting PERMANOVA with 99 perms with 1 processes
-#> 2023-05-15 21:22:34.605894 - Finished PERMANOVA
+#> 2023-05-16 14:37:53.680031 - Starting PERMANOVA with 99 perms with 1 processes
+#> 2023-05-16 14:37:53.786058 - Finished PERMANOVA
 
 # view the permanova results
 perm_get(aitchison_perm) %>% as.data.frame()
@@ -357,8 +357,8 @@ your permanova directly using the `ord_plot` function with constraints
 perm2 <- aitchison_dists %>%
   dist_permanova(variables = c("weight", "african", "sex"), seed = 321)
 #> Dropping samples with missings: 2
-#> 2023-05-15 21:22:34.623176 - Starting PERMANOVA with 999 perms with 1 processes
-#> 2023-05-15 21:22:36.280034 - Finished PERMANOVA
+#> 2023-05-16 14:37:53.808143 - Starting PERMANOVA with 999 perms with 1 processes
+#> 2023-05-16 14:37:56.526257 - Finished PERMANOVA
 ```
 
 We’ll visualise the effect of nationality and bodyweight on sample
@@ -451,12 +451,12 @@ and by participating in this project you agree to abide by its terms.
 ``` r
 sessionInfo()
 #> R version 4.3.0 (2023-04-21)
-#> Platform: aarch64-apple-darwin20 (64-bit)
+#> Platform: x86_64-apple-darwin20 (64-bit)
 #> Running under: macOS Ventura 13.3.1
 #> 
 #> Matrix products: default
-#> BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
-#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
+#> BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
+#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
 #> 
 #> locale:
 #> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -468,8 +468,8 @@ sessionInfo()
 #> [1] stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#> [1] ggplot2_3.4.2   dplyr_1.1.2     phyloseq_1.44.0 microViz_0.10.9
-#> [5] testthat_3.1.8  devtools_2.4.5  usethis_2.1.6  
+#> [1] ggplot2_3.4.2    dplyr_1.1.2      phyloseq_1.44.0  microViz_0.10.10
+#> [5] testthat_3.1.8   devtools_2.4.5   usethis_2.1.6   
 #> 
 #> loaded via a namespace (and not attached):
 #>   [1] RColorBrewer_1.1-3      shape_1.4.6             rstudioapi_0.14        
@@ -486,13 +486,13 @@ sessionInfo()
 #>  [34] shiny_1.7.4             digest_0.6.31           selectr_0.4-2          
 #>  [37] colorspace_2.1-0        S4Vectors_0.38.1        ps_1.7.5               
 #>  [40] pkgload_1.3.2           seriation_1.4.2         vegan_2.6-4            
-#>  [43] labeling_0.4.2          fansi_1.0.4             httr_1.4.5             
+#>  [43] labeling_0.4.2          fansi_1.0.4             httr_1.4.6             
 #>  [46] mgcv_1.8-42             compiler_4.3.0          remotes_2.4.2          
 #>  [49] doParallel_1.0.17       withr_2.5.0             viridis_0.6.3          
 #>  [52] pkgbuild_1.4.0          highr_0.10              MASS_7.3-60            
 #>  [55] sessioninfo_1.2.2       rjson_0.2.21            biomformat_1.28.0      
 #>  [58] permute_0.9-7           tools_4.3.0             ape_5.7-1              
-#>  [61] httpuv_1.6.9            glue_1.6.2              callr_3.7.3            
+#>  [61] httpuv_1.6.11           glue_1.6.2              callr_3.7.3            
 #>  [64] nlme_3.1-162            rhdf5filters_1.12.1     promises_1.2.0.1       
 #>  [67] gridtext_0.1.5          grid_4.3.0              Rtsne_0.16             
 #>  [70] cluster_2.1.4           reshape2_1.4.4          ade4_1.7-22            

tests/testthat/test-comp_barplot.R

@@ -5,6 +5,10 @@ test_that("comp_barplot throws correct errors", {
     object = comp_barplot(dietswap, tax_level = "geenus"),
     regexp = "must be the name of a valid rank"
   )
+  expect_error(
+    object = comp_barplot(dietswap, tax_level = ".Taxon"),
+    regexp = "'.Taxon' cannot be used as a rank name! You must rename that rank."
+  )
   expect_error(
     object = comp_barplot(dietswap, tax_level = "Genus", n_taxa = 1:15),
     regexp = "n_taxa must a positive integer"
@@ -28,14 +32,14 @@ test_that("fixing tax order of comp_barplot works", {
     comp_barplot(tax_level = "Phylum", n_taxa = 8, tax_order = fixed_order) +
     ggplot2::coord_flip()
 
-  expect_equal(levels(p8$data$Taxon), rev(fixed_order))
+  expect_equal(levels(p8$data$.Taxon), rev(fixed_order))
 
   p7 <- dietswap %>%
     ps_filter(timepoint == 1) %>%
     comp_barplot(tax_level = "Phylum", n_taxa = 7, tax_order = fixed_order) +
     ggplot2::coord_flip()
 
-  expect_equal(levels(p7$data$Taxon), rev(c(fixed_order[1:7], "Other")))
+  expect_equal(levels(p7$data$.Taxon), rev(c(fixed_order[1:7], "Other")))
 })
 
 # manual sample ordering -----------------------------------------------------
@@ -72,7 +76,7 @@ test_that("comp_barplot doesn't change", {
 
   expect_snapshot_csv(
     name = "unique_taxa_order",
-    object = levels(p$data$Taxon)
+    object = levels(p$data$.Taxon)
   )
   expect_snapshot_csv(
     name = "SAMPLE_order",
@@ -99,15 +103,15 @@ test_that("comp_barplot taxa ordering at level of 'unique' works", {
       tax_level = "unique", n_taxa = 8, sample_order = "asis", tax_order = sum,
       merge_other = FALSE
     )
-  expect_snapshot_csv(levels(p$data$Taxon), name = "uniqueTaxonLevelsUnmerged")
+  expect_snapshot_csv(levels(p$data$.Taxon), name = "uniqueTaxonLevelsUnmerged")
 
   p2 <- dietswap %>%
     ps_filter(timepoint == 1) %>%
     comp_barplot(
       tax_level = "unique", n_taxa = 3, sample_order = "asis", tax_order = sum,
       merge_other = TRUE
     )
-  expect_equal(object = levels(p2$data$Taxon), expected = c(
+  expect_equal(object = levels(p2$data$.Taxon), expected = c(
     "Other", "Oscillospira guillermondii et rel.",
     "Bacteroides vulgatus et rel.", "Prevotella melaninogenica et rel."
   ))
@@ -131,7 +135,7 @@ test_that("list of plots generated by group_by works", {
   for (p in names(plots)) {
     expect_snapshot_csv(
       name = paste0("unique_taxa_order-", p),
-      object = levels(plots[[p]]$data$Taxon)
+      object = levels(plots[[p]]$data$.Taxon)
     )
     expect_snapshot_csv(
       name = paste0("SAMPLE_order-", p),
@@ -151,7 +155,7 @@ test_that("list of plots generated by group_by works", {
       object = colnames(plots[[p]]$data),
       expected = c(
         "OTU", "Sample", "Abundance", "SAMPLE", "bmi_group", "Phylum",
-        "Family", "Genus", "unique", "Taxon"
+        "Family", "Genus", "unique", ".Taxon"
       )
     )
   }