Improve plotAbundance (#156)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.15.1
+Version: 1.15.2
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "tuomas.v.borman@utu.fi",
@@ -33,44 +33,46 @@ Encoding: UTF-8
 LazyData: false
 Depends:
     R (>= 4.0),
-    SummarizedExperiment,
-    TreeSummarizedExperiment,
-    mia (>= 1.13.0),
     ggplot2,
-    ggraph (>= 2.0)
+    ggraph (>= 2.0),
+    mia (>= 1.13.0),
+    SummarizedExperiment,
+    TreeSummarizedExperiment
 Imports:
-    methods,
-    stats,
-    S4Vectors,
+    ape,
     BiocGenerics,
     BiocParallel,
     DelayedArray,
-    scater,
-    ggtree,
+    DirichletMultinomial,
+    dplyr,
     ggnewscale,
-    viridis,
+    ggrepel,
+    ggplot2,
+    ggraph,
+    ggtree,
+    methods,
+    rlang,
+    scater,
+    S4Vectors,
+    SingleCellExperiment,
+    stats,
     tibble,
-    tidytext,
-    tidytree,
     tidygraph,
-    rlang,
-    purrr,
     tidyr,
-    dplyr,
-    ape,
-    DirichletMultinomial,
-    ggrepel,
-    SingleCellExperiment
+    tidytext,
+    tidytree,
+    viridis
 Suggests:
-    knitr,
-    rmarkdown,
     BiocStyle,
-    testthat,
-    patchwork,
-    vegan,
     bluster,
+    circlize,
     ComplexHeatmap,
-    circlize
+    ggh4x,
+    knitr,
+    patchwork,
+    rmarkdown,
+    testthat,
+    vegan
 Remotes:
     github::microbiome/miaTime
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -68,8 +68,11 @@ importFrom(ape,keep.tip)
 importFrom(ape,rotateConstr)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,all_of)
+importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,case_when)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,last_col)
@@ -78,6 +81,7 @@ importFrom(dplyr,n)
 importFrom(dplyr,pull)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
+importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
@@ -129,17 +133,18 @@ importFrom(mia,meltSE)
 importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,sym)
-importFrom(scater,plotExpression)
 importFrom(scater,plotReducedDim)
 importFrom(scater,retrieveCellInfo)
 importFrom(scater,retrieveFeatureInfo)
+importFrom(stats,formula)
 importFrom(stats,median)
 importFrom(stats,sd)
 importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)
 importFrom(tidygraph,activate)
 importFrom(tidygraph,as_tbl_graph)
 importFrom(tidygraph,as_tibble)
+importFrom(tidyr,complete)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,pivot_longer)
 importFrom(tidytext,reorder_within)

NEWS

@@ -32,4 +32,7 @@ Changes in version 1.13.x
 + Added getNeatOrder function
 + plotAbundance: enable plotting without agglomeration
 + Change parameter naming convention from parameter_name to parameter.name
-+ Added plotLoadings function
++ Added plotLoadings function
+
+Changes in version 1.15.x
++ plotAbundance: Improved visualization of sample metadata