From 4639b75d61cf2e5b6dffef73bc71a1970d8e8e4e Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Wed, 30 Aug 2023 16:51:02 -0400
Subject: [PATCH 1/5] allow return of indices of ordering for z score heatmap

---
 src/spikeanalysis/spike_plotter.py | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/spikeanalysis/spike_plotter.py b/src/spikeanalysis/spike_plotter.py
index beadec0..7c6b4df 100644
--- a/src/spikeanalysis/spike_plotter.py
+++ b/src/spikeanalysis/spike_plotter.py
@@ -66,7 +66,7 @@ def set_analysis(self, analysis: SpikeAnalysis):
             The SpikeAnalysis object for plotting
 
         """
-        assert isinstance(analysis, SpikeAnalysis), "analysis must be a SpikeAnaysis dataset"
+        assert isinstance(analysis, SpikeAnalysis), "analysis must be a SpikeAnalysis dataset"
         self.data = analysis
 
     def plot_zscores(
@@ -74,7 +74,8 @@ def plot_zscores(
         figsize: Optional[tuple] = (24, 10),
         sorting_index: Optional[int] = None,
         z_bar: Optional[list[int]] = None,
-    ):
+        indices: bool = False,
+    ) -> Optional[np.array]:
         """
         Function to plot heatmaps of z scored firing rate. All trial groups are plotted on the same axes.
         So it is best to have a figsize that wide to fit all different trial groups. In this plot each
@@ -89,7 +90,14 @@ def plot_zscores(
             The trial group to sort all values on. The default is None (which uses the largest trial group).
         z_bar: list[int]
             If given a list with min z score for the cbar at index 0 and the max at index 1. Overrides cbar generation
+        indices: bool, default False
+            If true will return the cluster ids sorted in the order they appear in the graph
 
+        Returns
+        -------
+        ordered_cluster_ids: np.array
+            if indices is True, the function will return the cluster ids as displayed in the z bar graph
+            
         """
 
         try:
@@ -214,6 +222,9 @@ def plot_zscores(
             if RESET_INDEX:
                 sorting_index = None
 
+        if indices:
+            return self.cluster_ids[z_score_sorting_index]
+
     def plot_raster(self, window: Union[list, list[list]]):
         """
         Function to plot rasters

From d2d0ab3dc76d32a4abb2e7742e0af6e08924e0b4 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Wed, 30 Aug 2023 16:53:00 -0400
Subject: [PATCH 2/5] fix typo

---
 src/spikeanalysis/spike_plotter.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/spikeanalysis/spike_plotter.py b/src/spikeanalysis/spike_plotter.py
index 7c6b4df..5e15241 100644
--- a/src/spikeanalysis/spike_plotter.py
+++ b/src/spikeanalysis/spike_plotter.py
@@ -223,7 +223,7 @@ def plot_zscores(
                 sorting_index = None
 
         if indices:
-            return self.cluster_ids[z_score_sorting_index]
+            return self.data.cluster_ids[z_score_sorting_index]
 
     def plot_raster(self, window: Union[list, list[list]]):
         """
@@ -234,8 +234,6 @@ def plot_raster(self, window: Union[list, list[list]]):
         window : Union[list, list[list]]
             The window [start, stop] to plot the raster over. Either one global list or nested list
             of [start, stop] format
-
-
         """
         from .analysis_utils import histogram_functions as hf
 

From c97dacba54f75602104c17aff6ca0b08aa4f7bb3 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Wed, 30 Aug 2023 16:54:17 -0400
Subject: [PATCH 3/5] up super minor version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b36d863..b5b3110 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "spikeanalysis"
-version = '0.0.8'
+version = '0.0.9'
 authors = [{name="Zach McKenzie", email="mineurs-torrent0x@icloud.com"}]
 description = "Analysis of Spike Trains"
 requires-python = ">=3.9"

From 9f6e6d459a0eff4ee7da742f5108c6165c0ecc93 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Wed, 30 Aug 2023 16:54:43 -0400
Subject: [PATCH 4/5] bump version in docs too

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 5fd6a08..8fc1cae 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -24,7 +24,7 @@
 author = "Zach McKenzie"
 
 # The full version, including alpha/beta/rc tags
-release = "0.0.8"
+release = "0.0.9"
 
 
 # -- General configuration ---------------------------------------------------

From bc05c34aab658d57a8c381b9e7aeaac4a1a7baf0 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Wed, 30 Aug 2023 16:58:56 -0400
Subject: [PATCH 5/5] linting

---
 src/spikeanalysis/spike_plotter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeanalysis/spike_plotter.py b/src/spikeanalysis/spike_plotter.py
index 5e15241..1022b92 100644
--- a/src/spikeanalysis/spike_plotter.py
+++ b/src/spikeanalysis/spike_plotter.py
@@ -97,7 +97,7 @@ def plot_zscores(
         -------
         ordered_cluster_ids: np.array
             if indices is True, the function will return the cluster ids as displayed in the z bar graph
-            
+
         """
 
         try: