update tutorial

broadinstitute · Nov 11, 2021 · 317c417 · 317c417
1 parent 19c60d1
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diff --git a/README.md b/README.md
@@ -27,9 +27,10 @@ To install Tangram, make sure you have [PyTorch](https://pytorch.org/) and [scan
 ```
 * install tangram-sc from shell:
 ```
+    conda activate tangram-env
     pip install tangram-sc
 ```
-* import tangram
+* To start using Tangram, import tangram in your jupyter notebooks or/and scripts 
 ```
     import tangram as tg
 ```

diff --git a/tangram/plot_utils.py b/tangram/plot_utils.py
@@ -178,7 +178,7 @@ def plot_cell_annotation_sc(
     x="x", 
     y="y", 
     spot_size=None, 
-    scale_factor=None, 
+    scale_factor=0.1, 
     perc=0,
     ax=None
 ):
@@ -317,7 +317,7 @@ def plot_genes_sc(
     x="x",
     y = "y",
     spot_size=None, 
-    scale_factor=None, 
+    scale_factor=0.1, 
     cmap="inferno", 
     perc=0,
     return_figure=False

diff --git a/tangram_tutorial.ipynb b/tangram_tutorial.ipynb