revise PSTH plot

kabilar · Jun 7, 2022 · 08cc600 · 08cc600
1 parent 5f1ef69
commit 08cc600
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Showing 4 changed files with 57 additions and 27 deletions.
diff --git a/notebooks/07-downstream-analysis.ipynb b/notebooks/07-downstream-analysis.ipynb
diff --git a/notebooks/py_scripts/07-downstream-analysis.py b/notebooks/py_scripts/07-downstream-analysis.py
@@ -8,9 +8,9 @@
 #       format_version: '1.5'
 #       jupytext_version: 1.13.7
 #   kernelspec:
-#     display_name: venv-nwb
+#     display_name: Python 3.8.11 ('ele')
 #     language: python
-#     name: venv-nwb
+#     name: python3
 # ---
 
 # + [markdown] tags=[]
@@ -110,9 +110,10 @@
 alignment_key = (event.AlignmentEvent & 'alignment_name = "center_button"'
                 ).fetch1('KEY')
 alignment_condition = {**clustering_key, **alignment_key, 
-                       'trial_condition': 'ctrl_center_button'}
+                       'trial_condition': 'ctrl_center_button',
+                       'bin_size':.2}
 analysis.SpikesAlignmentCondition.insert1(alignment_condition, skip_duplicates=True)
-
+alignment_condition.pop('bin_size')
 analysis.SpikesAlignmentCondition.Trial.insert(
     (analysis.SpikesAlignmentCondition * ctrl_trials & alignment_condition).proj(),
     skip_duplicates=True)
@@ -125,8 +126,11 @@
 # Now, let's create another set for the stimulus condition.
 # + a set of trials of interest to perform the analysis on - `stim` trials
 stim_trials = trial.Trial & clustering_key & 'trial_type = "stim"'
-alignment_condition = {**clustering_key, **alignment_key, 'trial_condition': 'stim_center_button'}
+alignment_condition = {**clustering_key, **alignment_key, 
+                       'trial_condition': 'stim_center_button',
+                       'bin_size':.2}
 analysis.SpikesAlignmentCondition.insert1(alignment_condition, skip_duplicates=True)
+alignment_condition.pop('bin_size')
 analysis.SpikesAlignmentCondition.Trial.insert(
     (analysis.SpikesAlignmentCondition * stim_trials & alignment_condition).proj(),
     skip_duplicates=True)
@@ -151,7 +155,15 @@
 # + a set of trials of interest to perform the analysis on - `stim` trials [markdown]
 # ## Visualize
 #
-# We can visualize the results with the `plot` function.
+# We can visualize the results with the `plot` function with our keys.
+# -
+
+clustering_key = (ephys.CuratedClustering 
+                  & {'subject': 'subject6', 'session_datetime': '2021-01-15 11:16:38',
+                     'insertion_number': 0}
+                 ).fetch1('KEY')
+alignment_key = (event.AlignmentEvent & 'alignment_name = "center_button"'
+                ).fetch1('KEY')
 
 # + a set of trials of interest to perform the analysis on - `stim` trials
 alignment_condition = {**clustering_key, **alignment_key, 'trial_condition': 'ctrl_center_button'}
@@ -162,4 +174,3 @@
 analysis.SpikesAlignment().plot(alignment_condition, unit=2);
 # -
 
-
diff --git a/workflow_array_ephys/analysis.py b/workflow_array_ephys/analysis.py
@@ -3,6 +3,7 @@
 
 from .pipeline import db_prefix, ephys, trial
 
+__all__ = ["db_prefix", "ephys", "trial", "event"]
 
 schema = dj.schema(db_prefix + 'analysis')
 
@@ -101,6 +102,7 @@ def plot(self, key, unit, axs=None):
         if axs is None:
             fig, axs = plt.subplots(2, 1, figsize=(12, 8))
 
+        bin_size = (SpikesAlignmentCondition & key).fetch1("bin_size")
         trial_ids, aligned_spikes = (self.AlignedTrialSpikes
                                      & key & {'unit': unit}
                                      ).fetch('trial_id', 'aligned_spike_times')
@@ -111,7 +113,7 @@ def plot(self, key, unit, axs=None):
 
         plot_psth._plot_spike_raster(aligned_spikes, trial_ids=trial_ids, ax=axs[0],
                                      title=f'{dict(**key, unit=unit)}', xlim=xlim)
-        plot_psth._plot_psth(psth, psth_edges, ax=axs[1],
+        plot_psth._plot_psth(psth, psth_edges, bin_size, ax=axs[1],
                              title='', xlim=xlim)
 
         return fig
diff --git a/workflow_array_ephys/plotting/plot_psth.py b/workflow_array_ephys/plotting/plot_psth.py
@@ -16,23 +16,23 @@ def _plot_spike_raster(aligned_spikes, trial_ids=None, vlines=[0], ax=None, titl
 
     assert len(raster) == len(trial_ids)
 
-    ax.plot(raster, trial_ids, 'r.', markersize=1)
+    ax.plot(raster, trial_ids, 'ro', markersize=4)
 
     for x in vlines:
         ax.axvline(x=x, linestyle='--', color='k')
 
     ax.set_ylabel('Trial (#)')
     if xlim:
         ax.set_xlim(xlim)
-    ax.set_axis_off()
+    # ax.set_axis_off()
     ax.set_title(title)
 
 
-def _plot_psth(psth, psth_edges, vlines=[0], ax=None, title='', xlim=None):
+def _plot_psth(psth, psth_edges, bin_size, vlines=[0], ax=None, title='', xlim=None):
     if not ax:
         fig, ax = plt.subplots(1, 1)
 
-    ax.plot(psth_edges, psth, 'r')
+    ax.bar(psth_edges, psth, width=bin_size, edgecolor="black", align="edge")
 
     for x in vlines:
         ax.axvline(x=x, linestyle='--', color='k')