From 91f301bd20483b75edf7cd635c13899737b027d3 Mon Sep 17 00:00:00 2001
From: Awni Mousa <awnimousa@gmail.com>
Date: Tue, 19 May 2020 20:40:35 -0400
Subject: [PATCH] Issue_33 and 31 fix

A fix related to https://github.com/dpeerlab/Palantir/issues/33 and https://github.com/dpeerlab/Palantir/issues/31
---
 README.md               | 15 ++++++++++++++-
 setup.py                |  4 +++-
 src/palantir/utils.py   | 12 +++++++++---
 src/palantir/version.py |  2 +-
 4 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index f0edde0b..b6b801bd 100755
--- a/README.md
+++ b/README.md
@@ -11,7 +11,8 @@ Palantir is an algorithm to align cells along differentiation trajectories. Pala
         $> pip install palantir
 
 2. Palantir depends on a number of `python3` packages available on pypi and these dependencies are listed in `setup.py`
-All the dependencies will be automatically installed using the above commands
+
+    All the dependencies will be automatically installed using the above commands
 
 3. To uninstall:
 		
@@ -19,7 +20,15 @@ All the dependencies will be automatically installed using the above commands
 
 4. If you would like to determine gene expression trends, please install <a href="https://cran.r-project.org"> R <a> programming language and the R package <a href="https://cran.r-project.org/web/packages/gam/">GAM </a>. You will also need to install the rpy2 module using 
 	
+		$> pip install .['PLOT_GENE_TRENDS']
+		    OR,
 		$> pip install rpy2
+	
+    In case of compiler error during installation of `rpy2`, try to link your compiler in `env`. Example:
+    
+        $> env CC=/usr/local/Cellar/gcc/xxx/bin/gcc-x pip install .['PLOT_GENE_TRENDS']
+
+    where `x` should be replaced with the version numbers
 		
 5. Palantir can also be used with [**Scanpy**](https://github.com/theislab/scanpy). It is fully integrated into Scanpy, and can be found under Scanpy's external modules ([link](https://scanpy.readthedocs.io/en/latest/api/scanpy.external.html#external-api))
 
@@ -70,6 +79,10 @@ ____
 Release Notes
 -------------
 
+### Version 0.2.6
+
+ * A fix to [issue#33](https://github.com/dpeerlab/Palantir/issues/33) and [issue#31](https://github.com/dpeerlab/Palantir/issues/31)
+ 
 ### Version 0.2.5
 
  * A fix related to [issue#28](https://github.com/dpeerlab/Palantir/issues/28). When identifying terminal states, duplicate values were generated instead of unique ones.
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 5c7ef5db..2006bf26 100755
--- a/setup.py
+++ b/setup.py
@@ -40,9 +40,11 @@
         "matplotlib>=2.2.2",
         "seaborn>=0.8.1",
         "tzlocal",
-        "rpy2>=3.0.2",
         "scanpy",
     ],
+    extras_require={
+        'PLOT_GENE_TRENDS': ["rpy2>=3.0.2"]
+    },
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
diff --git a/src/palantir/utils.py b/src/palantir/utils.py
index 4296900b..d3e533aa 100644
--- a/src/palantir/utils.py
+++ b/src/palantir/utils.py
@@ -22,11 +22,13 @@ def run_pca(data, n_components=300):
     return pca_projections, pca.explained_variance_ratio_
 
 
-def run_diffusion_maps(data_df, n_components=10, knn=30, n_jobs=-1, alpha=0):
+def run_diffusion_maps(data_df, n_components=10, knn=30, alpha=0):
     """Run Diffusion maps using the adaptive anisotropic kernel
 
-    :param data_df: PCA projections of the data or adjancency matrix
+    :param data_df: PCA projections of the data or adjacency matrix
     :param n_components: Number of diffusion components
+    :param knn: Number of nearest neighbors for graph construction
+    :param alpha: Normalization parameter for the diffusion operator
     :return: Diffusion components, corresponding eigen values and the diffusion operator
     """
 
@@ -36,7 +38,11 @@ def run_diffusion_maps(data_df, n_components=10, knn=30, n_jobs=-1, alpha=0):
         print("Determing nearest neighbor graph...")
         temp = sc.AnnData(data_df.values)
         sc.pp.neighbors(temp, n_pcs=0, n_neighbors=knn)
-        kNN = temp.uns["neighbors"]["distances"]
+        # maintaining backwards compatibility to Scanpy `sc.pp.neighbors`
+        try:
+            kNN = temp.uns["neighbors"]["distances"]
+        except KeyError:
+            kNN = temp.obsp['distances']
 
         # Adaptive k
         adaptive_k = int(np.floor(knn / 3))
diff --git a/src/palantir/version.py b/src/palantir/version.py
index 87fa5448..21a43d46 100644
--- a/src/palantir/version.py
+++ b/src/palantir/version.py
@@ -1,3 +1,3 @@
-__version__ = "0.2.5"
+__version__ = "0.2.6"
 __author__ = "Manu Setty"
 __author_email__ = "manu.talanki@gmail.com"