Workflow build fixes

microbiome · Aug 2, 2024 · 153df32 · 153df32
1 parent 56a25e1
commit 153df32
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Showing 4 changed files with 5 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.13.8
+Version: 1.13.9
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",

diff --git a/NAMESPACE b/NAMESPACE
@@ -136,6 +136,7 @@ importFrom(tidygraph,as_tbl_graph)
 importFrom(tidygraph,as_tibble)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,pivot_longer)
+importFrom(tidytext,scale_y_reordered)
 importFrom(tidytree,as.phylo)
 importFrom(tidytree,as.treedata)
 importFrom(tidytree,as_tibble)

diff --git a/R/plotLoadings.R b/R/plotLoadings.R
@@ -61,8 +61,6 @@
 #' library(mia)
 #' library(ggtree)
 #' library(scater)
-#' library(shadowtext)
-#' library(tidytext)
 #' data("GlobalPatterns", package = "mia")
 #' tse <- GlobalPatterns
 #' tse <- transformAssay(tse, method = "clr", pseudocount = 1)
@@ -149,7 +147,7 @@ setMethod("plotLoadings", signature = c(x = "TreeSummarizedExperiment"),
             # Ordering loadings and adding factor to keep the order
             df <- .get_loadings_plot_data(loadings_matrix, n, ncomponents)
             # Plot features with barplot layout
-            p <- .barplot_feature_loadings(df, layout, n, ncomponents)
+            p <- .barplot_feature_loadings(df)
         }
     return(p)
     }
@@ -395,7 +393,8 @@ setMethod("plotLoadings", signature = c(x = "SingleCellExperiment"),
     return(p)
 }
 
-.barplot_feature_loadings <- function(df, layout, n, ncomponents) {
+#' @importFrom tidytext scale_y_reordered
+.barplot_feature_loadings <- function(df) {
     cnames <- unique(df$PC)
     p <- ggplot(df, aes(x = Value, y = reorder_within(Feature, Value, PC))) +
         geom_bar(stat = "identity") +

diff --git a/man/plotLoadings.Rd b/man/plotLoadings.Rd