Merge reworked dynplot2

.Rbuildignore

@@ -9,3 +9,5 @@
 ^\.readme_files
 ^README
 ^tests
+^LICENSE\.md$
+^data-raw

DESCRIPTION

@@ -1,53 +1,61 @@
 Package: dynplot2
 Type: Package
-Title: Grammar of graphics for single-cell data
-Version: 1.0.0
+Title: Modular trajectory plotting
+Version: 1.1.0
 Authors@R: c(
   person("Robrecht", "Cannoodt", email = "[email protected]", role = c("aut")),
   person("Wouter", "Saelens", email = "[email protected]", role = c("aut", "cre")))
-Description: Package that create ggplot2 plots of single-cell datasets.
-License: GPL-3
+Description: Finetune visualisations of trajectories using ggplot2's grammar of graphics principles.
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 SystemRequirements: libudunits2-dev (deb) or udunits2-devel (rpm)
+URL: https://github.com/dynverse/dynplot2
+BugReports: https://github.com/dynverse/dynplot2/issues
 Depends:
   R (>= 3.0.0)
 Imports:
   assertthat,
   cowplot,
   dplyr,
+  digest,
   dynutils (>= 1.0.2),
   dynfeature (>= 1.0.0),
   dyndimred (>= 1.0.0),
   dynwrap (>= 1.0.0),
   GA,
   ggbeeswarm,
+  ggnewscale,
   ggplot2 (>= 3.0),
   ggraph,
   ggrepel,
+  grDevices,
   igraph,
   MASS,
   magrittr,
+  Matrix,
   methods,
   purrr,
-  rje,
-  shades,
+  reticulate,
+  rlang,
   RColorBrewer,
   reshape2,
+  scvelo,
+  shades,
+  stats,
+  stringr,
   testthat,
   tibble,
   tidyr,
   tidygraph,
+  utils,
   vipor,
   viridis
 Suggests:
   knitr,
   rmarkdown
-Remotes:  
-    dynverse/dynutils@master,
-    dynverse/dyndimred@master,
-    dynverse/dynwrap@master,
-    dynverse/dynfeature@master
+Remotes:
+  dynverse/scvelo@devel
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2014-2020
+COPYRIGHT HOLDER: Robrecht Cannoodt, Wouter Saelens

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2014-2020 Robrecht Cannoodt, Wouter Saelens
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,36 +1,55 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(ggplot_build,dynplot)
+export(color_milestone_percentages)
+export(define_milestone_colors)
 export(dynplot)
+export(dynplot_dendro)
+export(dynplot_dimred)
+export(dynplot_graph)
+export(dynplot_onedim)
 export(empty_plot)
+export(facet_grid_data)
+export(facet_wrap_data)
 export(geom_cell_hex)
 export(geom_cell_point)
-export(geom_expression_raster)
+export(geom_expression_tile)
+export(geom_feature_text)
 export(geom_milestone_label)
 export(geom_milestone_point)
 export(geom_trajectory_connection)
 export(geom_trajectory_divergence)
 export(geom_trajectory_segments)
 export(geom_velocity_arrow)
+export(geom_velocity_stream)
 export(get_features)
 export(get_milestone_palette_names)
-export(layout_dendro)
-export(layout_dimred)
-export(layout_graph)
 export(layout_heatmap)
 export(layout_modules)
-export(layout_onedim)
+export(milestone_palette)
+export(milestone_percentage_breaks)
 export(new_scale)
-export(new_scale_fillcolour)
-export(scale_expression_fillcolour)
-export(scale_milestones_fillcolour)
-export(select_expression)
-export(shadow)
+export(new_scale_color)
+export(new_scale_colour)
+export(new_scale_fill)
+export(scale_expression_color)
+export(scale_expression_colour)
+export(scale_expression_fill)
+export(scale_milestones_color)
+export(scale_milestones_colour)
+export(scale_milestones_fill)
+export(scale_velocity_color)
+export(scale_velocity_fill)
+export(scale_x_heatmap)
+export(select_feature_expression)
+export(select_feature_velocity)
+export(shadow_defaults)
 export(stat_velocity_cells)
 export(stat_velocity_grid)
 export(stat_velocity_random)
+export(stat_velocity_stream)
 export(theme_clean)
-export(theme_graph)
+export(theme_dynplot)
 import(dplyr)
 import(dyndimred)
 import(dynutils)
@@ -41,18 +60,29 @@ import(purrr)
 import(tibble)
 import(tidyr)
 importFrom(GA,ga)
+importFrom(Matrix,t)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(assertthat,assert_that)
+importFrom(grDevices,col2rgb)
 importFrom(grDevices,rainbow)
+importFrom(grDevices,rgb)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
-importFrom(rje,cubeHelix)
+importFrom(rlang,"%|%")
+importFrom(rlang,eval_tidy)
+importFrom(rlang,quo)
+importFrom(rlang,quo_text)
 importFrom(shades,hue)
 importFrom(stats,as.dendrogram)
 importFrom(stats,as.dist)
+importFrom(stats,cor)
 importFrom(stats,dist)
 importFrom(stats,hclust)
+importFrom(stats,kmeans)
 importFrom(stats,runif)
-importFrom(stringr,str_detect)
+importFrom(stringr,str_glue)
+importFrom(stringr,str_split)
+importFrom(utils,head)
+importFrom(utils,tail)

inst/NEWS.md → NEWS.md

@@ -1,3 +1,7 @@
+# dynplot2 1.0.0 (unreleased)
+
+ * Spin-off from dynplot, dynplot2 provides a more modular interface to visualize trajectories
+
 # dynplot 1.0.0 (28-03-2019)
 
  * Initial release of dynplot