Merge 17b66d7 into a1e9c2f

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 +65,11 @@ 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):
+                 overlay_values=False, colormap="vlag", save_dir=None, save_file=None):
     """Plots the z scores between all phenotypes as a clustermap.
 
     Args:
@@ -85,6 +89,9 @@ def draw_heatmap(data, x_labels, y_labels, dpi=None, center_val=None,
             color scheme for visualization
         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
@@ -101,7 +108,7 @@ def draw_heatmap(data, x_labels, y_labels, dpi=None, center_val=None,
         sns.clustermap(data_df, cmap=colormap, center=center_val)
 
     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"))
 
 

ark/phenotyping/consensus_cluster.R

@@ -36,6 +36,10 @@ clusterAvgPath <- args[6]
 # get consensus clustered write path
 pixelMatConsensus <- args[7]
 
+# set the random seed
+seed <- strtoi(args[8])
+set.seed(seed)
+
 # read cluster averaged data
 print("Reading cluster averaged data")
 clusterAvgs <- arrow::read_feather(clusterAvgPath)
@@ -46,7 +50,7 @@ clusterAvgsScale <- pmin(scale(clusterAvgs[markers]), cap)
 
 # run the consensus clustering
 print("Running consensus clustering")
-consensusClusterResults <- ConsensusClusterPlus(t(clusterAvgsScale), maxK=maxK)
+consensusClusterResults <- ConsensusClusterPlus(t(clusterAvgsScale), maxK=maxK, seed=seed)
 hClust <- consensusClusterResults[[maxK]]$consensusClass
 names(hClust) <- clusterAvgs$cluster
 

ark/phenotyping/create_som_matrix.R

@@ -34,6 +34,10 @@ normValsPath <- args[5]
 # get the weights write path
 pixelWeightsPath <- args[6]
 
+# set the random seed
+seed <- strtoi(args[7])
+set.seed(seed)
+
 # read the subsetted pixel mat data for training
 print("Reading the subsetted pixel matrix data for SOM training")
 pixelSubsetData <- NULL
@@ -76,7 +80,7 @@ arrow::write_feather(as.data.table(normVals), normValsPath)
 
 # run the SOM training step
 print("Run the SOM training")
-somResults <- SOM(data=pixelSubsetData, rlen=numPasses)
+somResults <- SOM(data=pixelSubsetData, rlen=numPasses, alpha=c(0.05, 0.01))
 
 # write the weights to HDF5
 print("Save trained weights")

ark/phenotyping/som_utils.py

@@ -9,27 +9,31 @@
 from skimage.io import imread
 
 import ark.settings as settings
+from ark.analysis import visualize
 from ark.utils import io_utils
 from ark.utils import load_utils
 from ark.utils import misc_utils
 
 
-def compute_cluster_avg(fovs, channels, base_dir,
-                        cluster_dir='pixel_mat_clustered',
-                        cluster_avg_name='pixel_cluster_avg.feather'):
-    """Averages channel values across all fovs in pixel_mat_clustered
+def compute_cluster_avg(fovs, channels, base_dir, cluster_col,
+                        cluster_dir='pixel_mat_clustered'):
+    """For each fov, compute the average channel values across each SOM cluster
 
     Args:
         fovs (list):
             The list of fovs to subset on
         channels (list):
             The list of channels to subset on
         base_dir (str):
-            Name of the directory to save the pixel files to
+            The path to the data directories
+        cluster_col (str):
+            Name of the column to group by
         cluster_dir (str):
             Name of the file containing the pixel data with cluster labels
-        cluster_avg_name (str):
-            Name of file to save the averaged results to
+
+    Returns:
+        pandas.DataFrame:
+            Contains the average channel values for each SOM cluster
     """
 
     # define the cluster averages DataFrame
@@ -42,8 +46,8 @@ def compute_cluster_avg(fovs, channels, base_dir,
         )
 
         # aggregate the sums and counts
-        sum_by_cluster = fov_pixel_data.groupby('cluster')[channels].sum()
-        count_by_cluster = fov_pixel_data.groupby('cluster')[channels].size().to_frame('count')
+        sum_by_cluster = fov_pixel_data.groupby(cluster_col)[channels].sum()
+        count_by_cluster = fov_pixel_data.groupby(cluster_col)[channels].size().to_frame('count')
 
         # concat the results together
         agg_results = pd.merge(
@@ -52,18 +56,15 @@ def compute_cluster_avg(fovs, channels, base_dir,
         cluster_avgs = pd.concat([cluster_avgs, agg_results])
 
     # sum the counts and the channel sums
-    sum_count_totals = cluster_avgs.groupby('cluster')[channels + ['count']].sum().reset_index()
+    sum_count_totals = cluster_avgs.groupby(cluster_col)[channels + ['count']].sum().reset_index()
 
     # now compute the means using the count column
     sum_count_totals[channels] = sum_count_totals[channels].div(sum_count_totals['count'], axis=0)
 
     # drop the count column
     sum_count_totals = sum_count_totals.drop('count', axis=1)
 
-    # save the DataFrame
-    feather.write_dataframe(sum_count_totals,
-                            os.path.join(base_dir, cluster_avg_name),
-                            compression='uncompressed')
+    return sum_count_totals
 
 
 def create_fov_pixel_data(fov, channels, img_data, seg_labels,
@@ -90,10 +91,10 @@ def create_fov_pixel_data(fov, channels, img_data, seg_labels,
 
     Returns:
         tuple:
-            A tuple containing two pd.Dataframes:
+            Contains the following:
 
-            - The full preprocessed pixel dataset for a fov
-            - The subsetted pixel dataset for a fov
+            - pandas.DataFrame: Gaussian blurred and channel sum normalized pixel data for a fov
+            - pandas.DataFrame: subset of the preprocessed pixel dataset for a fov
     """
 
     # for each marker, compute the Gaussian blur
@@ -129,21 +130,19 @@ def create_fov_pixel_data(fov, channels, img_data, seg_labels,
     return pixel_mat, pixel_mat_subset
 
 
-def create_pixel_matrix(fovs, channels, base_dir, tiff_dir, seg_dir,
+def create_pixel_matrix(fovs, base_dir, tiff_dir, seg_dir,
                         pre_dir='pixel_mat_preprocessed',
                         sub_dir='pixel_mat_subsetted', is_mibitiff=False,
                         blur_factor=2, subset_proportion=0.1, seed=42):
-    """Preprocess the images for FlowSOM clustering and creates a pixel-level matrix
+    """For each fov, add a Gaussian blur to each channel and normalize channel sums for each pixel
 
-    Saves preprocessed data to pre_dir and subsetted data to sub_dir
+    Saves data to pre_dir and subsetted data to sub_dir
 
     Args:
         fovs (list):
             List of fovs to subset over
-        channels (list):
-            List of channels to subset over
         base_dir (str):
-            Name of the directory to save the pixel files to
+            The path to the data directories
         tiff_dir (str):
             Name of the directory containing the tiff files
         seg_dir (str):
@@ -186,11 +185,11 @@ def create_pixel_matrix(fovs, channels, base_dir, tiff_dir, seg_dir,
         # load img_xr from MIBITiff or directory with the fov
         if is_mibitiff:
             img_xr = load_utils.load_imgs_from_mibitiff(
-                tiff_dir, mibitiff_files=[fov], channels=channels, dtype="int16"
+                tiff_dir, mibitiff_files=[fov], dtype="int16"
             )
         else:
             img_xr = load_utils.load_imgs_from_tree(
-                tiff_dir, fovs=[fov], channels=channels, dtype="int16"
+                tiff_dir, fovs=[fov], dtype="int16"
             )
 
         # load segmentation labels in for fov
@@ -201,7 +200,7 @@ def create_pixel_matrix(fovs, channels, base_dir, tiff_dir, seg_dir,
 
         # create the full and subsetted fov matrices
         pixel_mat, pixel_mat_subset = create_fov_pixel_data(
-            fov=fov, channels=channels, img_data=img_data, seg_labels=seg_labels,
+            fov=fov, channels=img_xr.channels.values, img_data=img_data, seg_labels=seg_labels,
             blur_factor=blur_factor, subset_proportion=subset_proportion, seed=seed
         )
 
@@ -222,7 +221,7 @@ def create_pixel_matrix(fovs, channels, base_dir, tiff_dir, seg_dir,
 
 def train_som(fovs, channels, base_dir,
               sub_dir='pixel_mat_subsetted', norm_vals_name='norm_vals.feather',
-              weights_name='weights.feather', num_passes=1):
+              weights_name='weights.feather', num_passes=1, seed=42):
     """Run the SOM training on the subsetted pixel data.
 
     Saves weights to base_dir/weights_name.
@@ -233,7 +232,7 @@ def train_som(fovs, channels, base_dir,
         channels (list):
             The list of markers to subset on
         base_dir (str):
-            The path to the data directory
+            The path to the data directories
         sub_dir (str):
             The name of the subsetted data directory
         norm_vals_name (str):
@@ -242,6 +241,8 @@ def train_som(fovs, channels, base_dir,
             The name of the weights file
         num_passes (int):
             The number of training passes to make through the dataset
+        seed (int):
+            The random seed to set for training
     """
 
     # define the paths to the data
@@ -266,7 +267,8 @@ def train_som(fovs, channels, base_dir,
 
     # run the SOM training process
     process_args = ['Rscript', '/create_som_matrix.R', ','.join(fovs), ','.join(channels),
-                    str(num_passes), subsetted_path, norm_vals_path, weights_path]
+                    str(num_passes), subsetted_path, norm_vals_path, weights_path, str(seed)]
+
     process = subprocess.Popen(process_args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
     # continuously poll the process for output/error to display in Jupyter notebook
@@ -365,16 +367,18 @@ def cluster_pixels(fovs, base_dir, pre_dir='pixel_mat_preprocessed',
 def consensus_cluster(fovs, channels, base_dir, max_k=20, cap=3,
                       cluster_dir='pixel_mat_clustered',
                       cluster_avg_name='pixel_cluster_avg.feather',
-                      consensus_dir='pixel_mat_consensus'):
+                      consensus_dir='pixel_mat_consensus', seed=42):
     """Run consensus clustering algorithm on summed data across channels
 
+    Saves data with consensus cluster labels to consensus_dir
+
     Args:
         fovs (list):
             The list of fovs to subset on
         channels (list):
             The list of channels to subset on
         base_dir (str):
-            Name of the directory to save the pixel files to
+            The path to the data directory
         max_k (int):
             The number of consensus clusters
         cap (int):
@@ -385,6 +389,8 @@ def consensus_cluster(fovs, channels, base_dir, max_k=20, cap=3,
             Name of file to save the channel-averaged results to
         consensus_dir (str):
             Name of directory to save the consensus clustered results
+        seed (int):
+            The random seed to set for consensus clustering
     """
 
     clustered_path = os.path.join(base_dir, cluster_dir)
@@ -396,15 +402,22 @@ def consensus_cluster(fovs, channels, base_dir, max_k=20, cap=3,
                                 (base_dir, clustered_path))
 
     # compute and write the averaged cluster results
-    compute_cluster_avg(fovs, channels, base_dir, cluster_dir)
+    cluster_avgs = compute_cluster_avg(fovs, channels, base_dir,
+                                       cluster_col='cluster', cluster_dir=cluster_dir)
+
+    # save the DataFrame
+    feather.write_dataframe(cluster_avgs,
+                            os.path.join(base_dir, cluster_avg_name),
+                            compression='uncompressed')
 
     # make consensus_dir if it doesn't exist
     if not os.path.exists(consensus_path):
         os.mkdir(consensus_path)
 
     # run the consensus clustering process
     process_args = ['Rscript', '/consensus_cluster.R', ','.join(fovs), ','.join(channels),
-                    str(max_k), str(cap), clustered_path, cluster_avg_path, consensus_path]
+                    str(max_k), str(cap), clustered_path, cluster_avg_path, consensus_path,
+                    str(seed)]
 
     process = subprocess.Popen(process_args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
@@ -418,3 +431,51 @@ def consensus_cluster(fovs, channels, base_dir, max_k=20, cap=3,
             break
         if output:
             print(output.strip())
+
+
+def visualize_cluster_data(fovs, channels, base_dir, cluster_dir, cluster_col='cluster',
+                           dpi=None, center_val=None, overlay_values=False, colormap="vlag",
+                           save_dir=None, save_file=None):
+    """Visualize the average cluster results for each cluster
+
+    Args:
+        fovs (list):
+            The list of fovs to subset on
+        channels (list):
+            The list of channels to subset on
+        base_dir (str):
+            The path to the data directories
+        cluster_dir (str):
+            Name of the directory containing the data to visualize
+        cluster_col (str):
+            Name of the column to group values by
+        dpi (float):
+            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
+        colormap (str):
+            color scheme for visualization
+        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
+    """
+
+    # average the channel values across the cluster column
+    cluster_avgs = compute_cluster_avg(fovs, channels, base_dir, cluster_col, cluster_dir)
+
+    # convert cluster column to integer type
+    cluster_avgs[cluster_col] = cluster_avgs[cluster_col].astype(int)
+
+    # sort cluster col in ascending order
+    cluster_avgs = cluster_avgs.sort_values(by=cluster_col)
+
+    # draw the heatmap
+    visualize.draw_heatmap(
+        data=cluster_avgs[channels].values, x_labels=cluster_avgs[cluster_col], y_labels=channels,
+        dpi=dpi, center_val=center_val, overlay_values=overlay_values,
+        colormap=colormap, save_dir=save_dir, save_file=save_file
+    )