Update 2.0.1

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.0.0
-Date: 2023-08-09 13:21:38 UTC
-SHA: aa0e071e38d4c36ab1357304b698d72ffac20e44
+Version: 2.0.1
+Date: 2023-08-13 10:28:15 UTC
+SHA: f88f6e19ce2d121e82869c4418d26fe9ff7b1db9

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: SCpubr
 Title: Generate Publication Ready Visualizations of Single Cell
     Transcriptomics Data
-Version: 2.0.0.9000
+Version: 2.0.1
 Authors@R: 
     person("Enrique", "Blanco-Carmona", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-1208-1691"))
@@ -75,10 +75,7 @@ Suggests:
     tidyr,
     UCell,
     viridis,
-    withr,
-    liana (>= 0.1.6)
-Remotes: 
-    saezlab/liana
+    withr
 VignetteBuilder: 
     knitr
 biocViews: Software, SingleCell, Visualization

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(do_AffinityAnalysisPlot)
 export(do_AlluvialPlot)
 export(do_BarPlot)
 export(do_BeeSwarmPlot)
@@ -10,7 +9,6 @@ export(do_ChordDiagramPlot)
 export(do_ColorPalette)
 export(do_CopyNumberVariantPlot)
 export(do_CorrelationPlot)
-export(do_DiffusionMapPlot)
 export(do_DimPlot)
 export(do_DotPlot)
 export(do_EnrichmentHeatmap)
@@ -20,17 +18,11 @@ export(do_FunctionalAnnotationPlot)
 export(do_GeyserPlot)
 export(do_GroupedGOTermPlot)
 export(do_GroupwiseDEPlot)
-export(do_LigandReceptorPlot)
-export(do_LoadingsPlot)
-export(do_MetadataPlot)
 export(do_NebulosaPlot)
 export(do_PathwayActivityPlot)
 export(do_RidgePlot)
-export(do_SCEnrichmentHeatmap)
-export(do_SCExpressionHeatmap)
 export(do_TFActivityPlot)
 export(do_TermEnrichmentPlot)
 export(do_ViolinPlot)
 export(do_VolcanoPlot)
 export(package_report)
-export(save_Plot)

NEWS.md

@@ -1,4 +1,24 @@
-# SCpubr v2.X.X (next release)
+# SCpbur v2.0.1 
+
+## General.
+-   Fixed a bug that prevented error messages stating the dependencies missing per function to show up properly.
+
+## do_BeeSwarmPlot()
+-   Changed default continuous palette to `YlGnBu`.
+-   Changed default legend title to `feature_to_rank` if `continous_feature = TRUE`. 
+-   Changed default value of `sequential.direction` to `1`. 
+-   Changed default value of `legend.position` to `bottom` when `continuous_feature = FALSE`. 
+
+## do_BoxPlot()
+-   Changed default value of `legend.position` to `bottom`. 
+-   Fixed a bug in which legend key glyphs would not show up when using `use_silhouette = TRUE`. 
+
+## do_ViolinPlot()
+-   Changed default value of `legend.position` to `bottom`. 
+-   Fixed a bug in which the default color palette would not be applied when `plot_boxplots = FALSE`.
+-   Added `legend.title.position` parameter and set it up as `top` by default.
+
+# SCpubr v2.0.1 
 
 ## General
 -   Refactored startup messages to comply with CRAN policies.
@@ -8,7 +28,7 @@
 
 ## `SCpubr::do_EnrichmentHeatmap`
 
--   Fixed a bug that checked the pacakge dependencies for the wrong function.
+-   Fixed a bug that checked the package dependencies for the wrong function.
 
 # SCpubr v2.0.0 
 
@@ -71,7 +91,6 @@ Many (except a few selected cases) of the functions that returned list of differ
 ## `SCpubr::do_BarPlot`
 
 -   Added `facet.by` parameter to extra group the bars by a third metadata variable.
--   Added `facet.by.direction` parameter to decide in which direction the facets are drawn.
 -   Added `order.by` to reorder the bars when using `position = fill` based on a value in `group.by`.
 -   Limited the possible interactions from `group.by`, `split.by` and `order.by` to those that make sense to plot. For instance, a bar plot using `group.by` and `position = fill` but not using `split.by ` resulted in bars of equal lenght with only one value per group of proportion `1`.
 -   Set default value of `plot.grid` to `FALSE`.