Merge branch 'master' into docker_windows

.gitignore

@@ -28,3 +28,4 @@ data/example_dataset/metaclustering/example_manually_adjust_metaclusters.ipynb
 Pipfile
 Pipfile.lock
 .coverage
+.python-version

.travis.yml

@@ -37,7 +37,8 @@ jobs:
       if: tag IS present
       python: 3.6
       script:
-        - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
+        - "travis_wait 20 sleep 1200 &"
+        - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin 
         - docker build -t "$TRAVIS_REPO_SLUG" .
         - docker tag "$TRAVIS_REPO_SLUG" "$TRAVIS_REPO_SLUG":latest
         - docker tag "$TRAVIS_REPO_SLUG" "$TRAVIS_REPO_SLUG":"${TRAVIS_TAG}"

Dockerfile

@@ -1,7 +1,7 @@
 FROM python:3.6
 
 # system maintenance
-RUN apt-get update && apt-get install -y gcc
+RUN apt-get update && apt-get install -y gcc r-base
 
 WORKDIR /scripts
 
@@ -16,5 +16,13 @@ COPY ark /opt/ark-analysis/ark
 # Install the package via setup.py
 RUN pip install /opt/ark-analysis
 
+# Install R dependency packages
+RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/BH/BH_1.75.0-0.tar.gz', repos=NULL, type='source')"
+RUN R -e "install.packages('arrow')"
+RUN R -e "install.packages('data.table')"
+RUN R -e "install.packages('BiocManager')"
+RUN R -e "BiocManager::install('FlowSOM')"
+RUN R -e "BiocManager::install('ConsensusClusterPlus')"
+
 # jupyter lab
 CMD jupyter lab --ip=0.0.0.0 --allow-root --no-browser --port=$JUPYTER_PORT --notebook-dir=/$JUPYTER_DIR

ark/analysis/visualize.py

@@ -7,7 +7,8 @@
 from ark.utils import misc_utils
 
 
-def draw_boxplot(cell_data, col_name, col_split=None, split_vals=None, dpi=None, save_dir=None):
+def draw_boxplot(cell_data, col_name, col_split=None,
+                 split_vals=None, dpi=None, save_dir=None, save_file=None):
     """Draws a boxplot for a given column, optionally with help from a split column
 
     Args:
@@ -23,6 +24,9 @@ def draw_boxplot(cell_data, col_name, col_split=None, split_vals=None, dpi=None,
             The resolution of the image to save, ignored if save_dir is None
         save_dir (str):
             If specified, a directory where we will save the plot
+        save_file (str):
+            If save_dir specified, specify a file name you wish to save to.
+            Ignored if save_dir is None
     """
 
     # the col_name must be valid
@@ -61,11 +65,12 @@ def draw_boxplot(cell_data, col_name, col_split=None, split_vals=None, dpi=None,
 
     # save visualization to a directory if specified
     if save_dir is not None:
-        misc_utils.save_figure(save_dir, "boxplot_viz.png", dpi=dpi)
+        misc_utils.save_figure(save_dir, save_file, dpi=dpi)
 
 
-def draw_heatmap(data, x_labels, y_labels, dpi=None, center_val=None,
-                 overlay_values=False, colormap="vlag", save_dir=None):
+def draw_heatmap(data, x_labels, y_labels, dpi=None, center_val=None, min_val=None, max_val=None,
+                 cbar_ticks=None, colormap="vlag", row_colors=None, row_cluster=True,
+                 col_colors=None, col_cluster=True, save_dir=None, save_file=None):
     """Plots the z scores between all phenotypes as a clustermap.
 
     Args:
@@ -79,12 +84,27 @@ def draw_heatmap(data, x_labels, y_labels, dpi=None, center_val=None,
             The resolution of the image to save, ignored if save_dir is None
         center_val (float):
             value at which to center the heatmap
-        overlay_values (bool):
-            whether to overlay the raw heatmap values on top
+        min_val (float):
+            minimum value the heatmap should take
+        max_val (float):
+            maximum value the heatmap should take
+        cbar_ticks (int):
+            list of values containing tick labels for the heatmap colorbar
         colormap (str):
             color scheme for visualization
+        row_colors (list):
+            Include these values as an additional color-coded cluster bar for row values
+        row_cluster (bool):
+            Whether to include dendrogram clustering for the rows
+        col_colors (list):
+            Include these values as an additional color-coded cluster bar for column values
+        col_cluster (bool):
+            Whether to include dendrogram clustering for the columns
         save_dir (str):
             If specified, a directory where we will save the plot
+        save_file (str):
+            If save_dir specified, specify a file name you wish to save to.
+            Ignored if save_dir is None
     """
 
     # Replace the NA's and inf values with 0s
@@ -95,13 +115,14 @@ def draw_heatmap(data, x_labels, y_labels, dpi=None, center_val=None,
     data_df = pd.DataFrame(data, index=x_labels, columns=y_labels)
     sns.set(font_scale=.7)
 
-    if overlay_values:
-        sns.clustermap(data_df, cmap=colormap, annot=data, center=center_val)
-    else:
-        sns.clustermap(data_df, cmap=colormap, center=center_val)
+    sns.clustermap(
+        data_df, cmap=colormap, center=center_val,
+        vmin=min_val, vmax=max_val, row_colors=row_colors, row_cluster=row_cluster,
+        col_colors=col_colors, col_cluster=col_cluster, cbar_kws={'ticks': cbar_ticks}
+    )
 
     if save_dir is not None:
-        misc_utils.save_figure(save_dir, "z_score_viz.png", dpi=dpi)
+        misc_utils.save_figure(save_dir, save_file, dpi=dpi)
 
 
 def get_sorted_data(cell_data, sort_by_first, sort_by_second, is_normalized=False):

ark/analysis/visualize_test.py

@@ -29,7 +29,7 @@ def test_draw_heatmap():
 
         # test that with save_dir, we do save
         visualize.draw_heatmap(z, pheno_titles, pheno_titles,
-                               save_dir=temp_dir)
+                               save_dir=temp_dir, save_file="z_score_viz.png")
         assert os.path.exists(os.path.join(temp_dir, "z_score_viz.png"))
 
 
@@ -66,7 +66,7 @@ def test_draw_boxplot():
     with tempfile.TemporaryDirectory() as temp_dir:
         visualize.draw_boxplot(cell_data=random_data, col_name="A",
                                col_split=settings.PATIENT_ID, split_vals=[1, 2],
-                               save_dir=temp_dir)
+                               save_dir=temp_dir, save_file="boxplot_viz.png")
         assert os.path.exists(os.path.join(temp_dir, "boxplot_viz.png"))