Merge pull request #7 from KrishnaswamyLab/dev

Use Python PHATE with reticulate

.Rbuildignore

@@ -1,4 +1,18 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^data-raw$
+^.*\.Rproj$         # Automatically added by RStudio,
+^\.Rproj\.user$     # used for temporary files.
+^data-raw$          # raw data generation code
+^README\.Rmd$       # An Rmarkdown file used to generate README.md
+^cran-comments\.md$ # Comments for CRAN submission
+^NEWS\.md$          # A news file written in Markdown
+^\.travis\.yml$     # Used for continuous integration testing with travis
+^desktop\.ini$      # Windows detritus
+^R/desktop\.ini$    # Windows detritus
+^man/desktop\.ini$  # Windows detritus
+^data/desktop\.ini$ # Windows detritus
+^\.git$             # git repository
+^desktop\.ini$
+^phater\.Rproj$
 ^README\.Rmd$
+^data/desktop\.ini$
+^\.git$
+^\.git/*$

DESCRIPTION

@@ -1,26 +1,26 @@
 Package: phater
-Title: PHATE - Potential of Heat-diffusion for Affinity-based Transition Embedding
-Version: 0.2
-Authors@R: person("Krishnan", "Srinivasan", email = "[email protected]", role = c("aut", "cre"))
+Title: PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding
+Version: 0.2.5
+Authors@R: c(person("Krishnan", "Srinivasan", email = "[email protected]", role = c("aut")),
+             person(given = 'Scott', family = 'Gigante', email = '[email protected]', role = 'cre', comment = c(ORCID = '0000-0002-4544-2764')))
 Description: PHATE is a tool for visualizing high dimensional single-cell data
   with natural progressions or trajectories. PHATE uses a novel conceptual framework
   for learning and visualizing the manifold inherent to biological systems in which
   smooth transitions mark the progressions of cells from one state to another.
   To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic
-  stem cells, human embryonic stem cells, and bone marrow samples, check out our preprint on BioRxiv.
-  http://biorxiv.org/content/early/2017/03/24/120378
-License: GPL-2
+  stem cells, human embryonic stem cells, and bone marrow samples, check out our preprint on BioRxiv
+  at <http://biorxiv.org/content/early/2017/03/24/120378>.
+License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends:
-    R (>= 3.3.2),
-    ggplot2
+    R (>= 3.3)
 Imports:
-    expm (>= 0.999),
-    smacof (>= 1.10-5),
+    methods,
+    stats,
+    graphics,
+    reticulate (>= 1.7),
     Matrix (>= 1.2-12),
-    FNN (>= 1.1),
-    irlba (>= 2.3.1),
     ggplot2
 Suggests:
     gridGraphics,

NAMESPACE

@@ -6,5 +6,7 @@ S3method(ggplot,phate)
 S3method(plot,phate)
 S3method(print,phate)
 S3method(summary,phate)
+export(install.phate)
 export(library.size.normalize)
 export(phate)
+importFrom(ggplot2,ggplot)