fix readme indents

README.md

@@ -45,15 +45,15 @@ MAGIC has been implemented in Python, Matlab, and R.
 
 To install with `pip`, run the following from a terminal:
 
-        pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
+    pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
 
 #### Installation from GitHub
 
 To clone the repository and install manually, run the following from a terminal:
 
-        git clone git://github.com/KrishnaswamyLab/MAGIC.git
-        cd MAGIC/python
-        python setup.py install --user
+    git clone git://github.com/KrishnaswamyLab/MAGIC.git
+    cd MAGIC/python
+    python setup.py install --user
 
 ### Usage
 
@@ -95,9 +95,9 @@ To use MAGIC, you will need to install both the R and Python packages.
 
 You can install `Rmagic` with `devtools` by running the following in R:
 
-        if (!require(devtools)) install.packages("devtools")
-        library(devtools)
-        install_github("KrishnaswamyLab/magic/Rmagic")
+    if (!require(devtools)) install.packages("devtools")
+    library(devtools)
+    install_github("KrishnaswamyLab/magic/Rmagic")
 
 You then need to install MAGIC in Python with `pip` by running the following from a terminal:
 
@@ -109,11 +109,11 @@ If `python` or `pip` are not installed, you will need to install them. We recomm
 
 To clone the repository and install manually, run the following from a terminal:
 
-        git clone git://github.com/KrishnaswamyLab/MAGIC.git
-        cd MAGIC/python
-        python setup.py install --user
-        cd ../Rmagic
-        R CMD INSTALL .
+    git clone git://github.com/KrishnaswamyLab/MAGIC.git
+    cd MAGIC/python
+    python setup.py install --user
+    cd ../Rmagic
+    R CMD INSTALL .
 
 ### Usage
 

python/README.md

@@ -24,31 +24,31 @@ For R and MATLAB implementations of MAGIC, see <https://github.com/KrishnaswamyL
 
 To install with `pip`, run the following from a terminal:
 
-        pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
+    pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python
 
 #### Installation from GitHub
 
 To clone the repository and install manually, run the following from a terminal:
 
-        git clone git://github.com/KrishnaswamyLab/MAGIC.git
-        cd MAGIC/python
-        python setup.py install --user
+    git clone git://github.com/KrishnaswamyLab/MAGIC.git
+    cd MAGIC/python
+    python setup.py install --user
 
 ### Usage
 
 ##### Example data
 
 The following code runs MAGIC on test data located in the MAGIC repository.
 
-		import magic
-		import pandas as pd
-		import matplotlib.pyplot as plt
-		X = pd.read_csv("MAGIC/data/test_data.csv")
-		magic_operator = magic.MAGIC()
-		X_magic = magic_operator.fit_transform(X, genes=['VIM', 'CDH1', 'ZEB1'])
-		plt.scatter(X_magic['VIM'], X_magic['CDH1'], c=X_magic['ZEB1'], s=1, cmap='inferno')
-		plt.show()
-		magic.plot.animate_magic(X, gene_x='VIM', gene_y='CDH1', gene_color='ZEB1', operator=magic_operator)
+	import magic
+	import pandas as pd
+	import matplotlib.pyplot as plt
+	X = pd.read_csv("MAGIC/data/test_data.csv")
+	magic_operator = magic.MAGIC()
+	X_magic = magic_operator.fit_transform(X, genes=['VIM', 'CDH1', 'ZEB1'])
+	plt.scatter(X_magic['VIM'], X_magic['CDH1'], c=X_magic['ZEB1'], s=1, cmap='inferno')
+	plt.show()
+	magic.plot.animate_magic(X, gene_x='VIM', gene_y='CDH1', gene_color='ZEB1', operator=magic_operator)
 
 ##### Interactive command line
 We have included two tutorial notebooks on MAGIC usage and results visualization for single cell RNA-seq data.