plotRDA (#87)

* Initialise plotRDA

* up

* up

* up

* up

* Match dot and ellipse colours

* Add arguments for ellipse, vector and text aesthetics

* plotRDA -> Add option to turn off text repel and catch all ggrepel args

* up

* Catch all params for plotReducedDim

* up

* Update plotRDA vignettes

* Make alias plotCCA for plotRDA

* Use retrieveCellInfo in plotRDA

* Remove remnants of conflicts

* Implement method of plotRDA for rda/cca object and extend vignettes

* Streamline plotRDA code

* Catch all args in setGeneric and setMethod of plotRDA

* Minor fixes

* Update plotRDA docs and check input params

* Fix build for plotRDA

* Update docs on plotRDA

* Import SingleCellExperiment in DESCRIPTION

* Fix DESCRIPTION

* Update plotRDA examples

* Fix plotRDA docs

* Debug and add signif/variance args to plotRDA

* Implement add.ellipse arg in plotRDA

* Update plotRDA vignettes

* Bump version and add news

* Initiate tests for plotRDA and correct version

* Implement unit tests for plotRDA

* up

---------

Co-authored-by: Giulio Benedetti <[email protected]>

.Rbuildignore

@@ -5,3 +5,5 @@
 .RData
 .pdf
 inst/extras/
+^doc$
+^Meta$

.gitignore

@@ -3,3 +3,6 @@ inst/doc
 docs
 .Rhistory
 *.RData
+.DS_Store
+/doc/
+/Meta/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.9.2
+Version: 1.9.3
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -11,7 +11,10 @@ Authors@R:
       person(given = "Leo", family = "Lahti", role = c("aut"),
              email = "[email protected]",
              comment = c(ORCID = "0000-0001-5537-637X")),
-      person(given = "Basil", family = "Courbayre", role = c("ctb"))
+      person(given = "Basil", family = "Courbayre", role = c("ctb")),
+      person(given = "Giulio", family = "Benedetti", role = c("ctb"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-8732-7692"))
 	     )
 Description: The miaViz package implements functions to visualize
     TreeSummarizedExperiment objects especially in the context of microbiome
@@ -46,7 +49,9 @@ Imports:
     tidyr,
     dplyr,
     ape,
-    DirichletMultinomial
+    DirichletMultinomial,
+    ggrepel,
+    SingleCellExperiment
 Suggests:
     knitr,
     rmarkdown,

NAMESPACE

@@ -1,11 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 export(plotAbundanceDensity)
+export(plotCCA)
 export(plotColGraph)
 export(plotColTile)
 export(plotDMNFit)
 export(plotPrevalence)
 export(plotPrevalentAbundance)
+export(plotRDA)
 export(plotRowGraph)
 export(plotRowTile)
 export(plotSeries)
@@ -16,12 +18,14 @@ exportMethods(colTreeData)
 exportMethods(combineTreeData)
 exportMethods(plotAbundance)
 exportMethods(plotAbundanceDensity)
+exportMethods(plotCCA)
 exportMethods(plotColGraph)
 exportMethods(plotColTile)
 exportMethods(plotColTree)
 exportMethods(plotDMNFit)
 exportMethods(plotPrevalence)
 exportMethods(plotPrevalentAbundance)
+exportMethods(plotRDA)
 exportMethods(plotRowGraph)
 exportMethods(plotRowTile)
 exportMethods(plotRowTree)
@@ -45,6 +49,8 @@ importFrom(DelayedArray,rowMeans)
 importFrom(DelayedArray,rowSums)
 importFrom(DirichletMultinomial,mixture)
 importFrom(S4Vectors,metadata)
+importFrom(SingleCellExperiment,reducedDim)
+importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
@@ -90,6 +96,8 @@ importFrom(ggplot2,scale_y_discrete)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
+importFrom(ggrepel,geom_label_repel)
+importFrom(ggrepel,geom_text_repel)
 importFrom(ggtree,geom_cladelab)
 importFrom(ggtree,geom_highlight)
 importFrom(ggtree,geom_nodelab)
@@ -105,6 +113,7 @@ importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,sym)
 importFrom(scater,plotExpression)
+importFrom(scater,plotReducedDim)
 importFrom(scater,retrieveCellInfo)
 importFrom(scater,retrieveFeatureInfo)
 importFrom(stats,sd)

NEWS

@@ -19,4 +19,5 @@ Changes in version 1.7.x
 + Fixed plotGraph* that was broked due changes in dependencies
 
 Changes in version 1.9.x
-+ Updated plotDMN to work with newest mia version
++ Updated plotDMN to work with newest mia version
++ Added plotCCA and plotRDA functions