From 2a1db6d1c2332d81b1789852c7c3fdd88d2041d9 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Tue, 25 May 2021 21:39:25 -0400
Subject: [PATCH 01/23] Start work on function to plot connectivity matrix with
 weights

---
 hnn_core/viz.py | 73 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 520590965..c2e461cd8 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -569,6 +569,75 @@ def plot_cell_morphology(cell, ax, show=True):
     return ax
 
 
+def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
+    """ Plot connectivity matrix with color bar for synaptic weights
+    Parameters
+    ----------
+    net : Instance of Network object
+        The Network object
+    conn_idx : int
+        Index of _Connectivity object to be visualized
+        from `net.connectivity`
+    ax : instance of Axes3D
+        Matplotlib 3D axis
+    show : bool
+        If True, show the plot
+
+    Returns
+    -------
+    fig : instance of matplotlib Figure
+        The matplotlib figure handle.
+    """
+    import matplotlib.pyplot as plt
+    from .network import Network
+
+    if not isinstance(net, Network):
+        raise TypeError('conn must be instance of _Connectivity')
+    if ax is None:
+        _, ax = plt.subplots(1, 1)
+
+    # Load objects for distance calculation
+    conn = net.connectivity[conn_idx]
+    nc_dict = conn['nc_dict']
+    src_type = conn['src_type']
+    target_type = conn['target_type']
+    src_type_pos = net.pos_dict[src_type]
+    target_type_pos = net.pos_dict[target_type]
+
+    src_range = np.array(conn['src_range'])
+    target_range = np.array(conn['target_range'])
+    connectivity_matrix = np.zeros((len(src_range), len(target_range)))
+
+    for src_gid, target_src_pair in conn['gid_pairs'].items():
+        src_idx = np.where(src_range == src_gid)[0][0]
+        target_indeces = np.where(np.in1d(target_range, target_src_pair))[0]
+        for target_idx in target_indeces:
+            src_pos = src_type_pos[src_idx]
+            target_pos = target_type_pos[target_idx]
+
+            # Identical calculation used in Cell.par_connect_from_src()
+            dx = src_pos[0] - target_pos[0]
+            dy = src_pos[1] - target_pos[1]
+            d = np.sqrt(dx**2 + dy**2)
+
+            weight = nc_dict['A_weight'] * \
+                np.exp(-(d**2) / (nc_dict['lamtha']**2))
+
+            connectivity_matrix[src_idx, target_idx] = weight
+
+    ax.imshow(connectivity_matrix, cmap='Greys', interpolation='none')
+    ax.set_xlabel(f"{conn['target_type']} target gids "
+                  f"({target_range[0]}-{target_range[-1]})")
+    ax.set_xticklabels(list())
+    ax.set_ylabel(f"{conn['src_type']} source gids "
+                  f"({src_range[0]}-{src_range[-1]})")
+    ax.set_yticklabels(list())
+    ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
+                 f"({conn['loc']}, {conn['receptor']})")
+
+    return ax.get_figure()
+
+
 def plot_connectivity_matrix(conn, ax=None, show=True):
     """Plot connectivity matrix for instance of _Connectivity object.
 
@@ -576,6 +645,10 @@ def plot_connectivity_matrix(conn, ax=None, show=True):
     ----------
     conn : Instance of _Connectivity object
         The _Connectivity object
+    ax : instance of Axes3D
+        Matplotlib 3D axis
+    show : bool
+        If True, show the plot
 
     Returns
     -------

From 31f2f4ce2ce3e66ccf1b91cd13edbdb4a196a57d Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Tue, 25 May 2021 21:39:56 -0400
Subject: [PATCH 02/23] Add plot_connectivity_weights to example

---
 examples/plot_connectivity.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index 5c7824e98..67b287da1 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -38,10 +38,16 @@
 # Instantiating the network comes with a predefined set of connections that
 # reflect the canonical neocortical microcircuit. ``net.connectivity``
 # is a list of dictionaries which detail every cell-cell, and drive-cell
-# connection.
-print(len(net_erp.connectivity))
+# connection. The weights of these connections can be visualized with
+# :func:`~hnn_core.viz.plot_connectivity_weights`
+from hnn_core.viz import plot_connectivity_weights
+n_connections = len(net_erp.connectivity)
+print(n_connections)
 print(net_erp.connectivity[0:2])
 
+# Plot the last connection added to the network
+plot_connectivity_weights(net_erp, conn_idx=n_connections)
+
 ###############################################################################
 # Data recorded during simulations are stored under
 # :class:`~hnn_core.Cell_Response`. Spiking activity can be visualized after
@@ -118,6 +124,7 @@
 net_sparse.connectivity[-2].plot()
 net_sparse.connectivity[-1].plot()
 
+
 ###############################################################################
 # Using the sparse connectivity pattern produced a lot more spiking in
 # the L5 pyramidal cells. Nevertheless there appears to be some rhythmicity

From e54f8bada2591ecba581af5c2e157f48638d4f09 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Tue, 25 May 2021 21:45:28 -0400
Subject: [PATCH 03/23] Better plots

---
 examples/plot_connectivity.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index 67b287da1..640e76de0 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -8,7 +8,7 @@
 
 # Author: Nick Tolley <nicholas_tolley@brown.edu>
 
-# sphinx_gallery_thumbnail_number = 5
+# sphinx_gallery_thumbnail_number = 1
 
 import os.path as op
 
@@ -41,12 +41,13 @@
 # connection. The weights of these connections can be visualized with
 # :func:`~hnn_core.viz.plot_connectivity_weights`
 from hnn_core.viz import plot_connectivity_weights
-n_connections = len(net_erp.connectivity)
-print(n_connections)
-print(net_erp.connectivity[0:2])
+print(len(net_erp.connectivity))
 
-# Plot the last connection added to the network
-plot_connectivity_weights(net_erp, conn_idx=n_connections)
+print(net_erp.connectivity[15])
+plot_connectivity_weights(net_erp, conn_idx=15)
+
+print(net_erp.connectivity[20])
+plot_connectivity_weights(net_erp, conn_idx=20)
 
 ###############################################################################
 # Data recorded during simulations are stored under

From a27426158d14aa6aeb6e585169f13e85c4467a58 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Tue, 25 May 2021 21:45:54 -0400
Subject: [PATCH 04/23] Show plots

---
 hnn_core/viz.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index c2e461cd8..0a7b67add 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -635,6 +635,7 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
     ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
                  f"({conn['loc']}, {conn['receptor']})")
 
+    plt_show(show)
     return ax.get_figure()
 
 

From 9e548efef7ed4e7c6a11a6647aebfcb31d5410f8 Mon Sep 17 00:00:00 2001
From: Nick Tolley <55253912+ntolley@users.noreply.github.com>
Date: Thu, 27 May 2021 16:27:51 -0400
Subject: [PATCH 05/23] Update hnn_core/viz.py

Co-authored-by: Mainak Jas <jasmainak@users.noreply.github.com>
---
 hnn_core/viz.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 0a7b67add..75f536537 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -570,7 +570,8 @@ def plot_cell_morphology(cell, ax, show=True):
 
 
 def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
-    """ Plot connectivity matrix with color bar for synaptic weights
+    """Plot connectivity matrix with color bar for synaptic weights
+
     Parameters
     ----------
     net : Instance of Network object

From b5e32a5e4639d843d1e5e819d4a2517590c00a74 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 27 May 2021 17:22:33 -0400
Subject: [PATCH 06/23] Move gaussian decay calculations into separate
 functions

---
 hnn_core/cell.py | 77 +++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 63 insertions(+), 14 deletions(-)

diff --git a/hnn_core/cell.py b/hnn_core/cell.py
index d1d6dff2a..d910e4c38 100644
--- a/hnn_core/cell.py
+++ b/hnn_core/cell.py
@@ -25,6 +25,66 @@ def _get_cos_theta(p_secs, sec_name_apical):
     return cos_thetas
 
 
+def _calculate_gaussian(x_val, height, lamtha):
+    """Return height of gaussian at x_val.and
+
+    Parameters
+    ----------
+    x_val : float
+        Value on x-axis to query height of gaussian curve.
+    height : float
+        Height of the gaussian curve at zero.
+    lamtha : float
+        Space constant.
+
+    Returns
+    -------
+    x_height : float
+        Height of gaussian at x_val.
+
+    Notes
+    -----
+    Gaussian curve is centered at zero and has a fixed peak height
+    such the _calculate_gaussian(0, lamtha) returns 1 for all lamtha.
+    """
+    x_height = height * np.exp(-(x_val**2) / (lamtha**2))
+
+    return x_height
+
+
+def _get_gaussian_connection(nc_dict, target_pos):
+    """Calculate distance dependent connection properties.
+
+    Parameters
+    ----------
+    nc_dict : dict
+        Dictionary with keys: pos_src, A_weight, A_delay, lamtha
+        Defines the connection parameters
+    target_pos : float
+        Position of target cell.
+
+    Returns
+    -------
+    weight : float
+        Weight of the synaptic connection.
+    delay : float
+        Delay of synaptic connection.
+
+    Notes
+    -----
+    Distance in xy plane is used for gaussian decay.
+    """
+    x_dist = target_pos[0] - nc_dict['pos_src'][0]
+    y_dist = target_pos[1] - nc_dict['pos_src'][1]
+    cell_dist = np.sqrt(x_dist**2 + y_dist**2)
+
+    weight = _calculate_gaussian(
+        cell_dist, nc_dict['A_weight'], nc_dict['lamtha'])
+    delay = _calculate_gaussian(
+        cell_dist, nc_dict['A_delay'], nc_dict['lamtha'])
+    return weight, delay
+
+
 class _ArtificialCell:
     """The ArtificialCell class for initializing a NEURON feed source.
 
@@ -477,24 +537,13 @@ def parconnect_from_src(self, gid_presyn, nc_dict, postsyn):
         from .network_builder import _PC
 
         nc = _PC.gid_connect(gid_presyn, postsyn)
-        # calculate distance between cell positions with pardistance()
-        d = self._pardistance(nc_dict['pos_src'])
-        # set props here
+
+        # set props here.
         nc.threshold = nc_dict['threshold']
-        nc.weight[0] = nc_dict['A_weight'] * \
-            np.exp(-(d**2) / (nc_dict['lamtha']**2))
-        nc.delay = nc_dict['A_delay'] / \
-            (np.exp(-(d**2) / (nc_dict['lamtha']**2)))
+        nc.weight[0], nc.delay = _get_gaussian_connection(nc_dict, self.pos)
 
         return nc
 
-    # pardistance function requires pre position, since it is
-    # calculated on POST cell
-    def _pardistance(self, pos_pre):
-        dx = self.pos[0] - pos_pre[0]
-        dy = self.pos[1] - pos_pre[1]
-        return np.sqrt(dx**2 + dy**2)
-
     def plot_morphology(self, ax=None, cell_types=None, show=True):
         """Plot the cell morphology.
 

From 8444d11969541ef5d3214fcfe85fd1e15b13a54f Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 27 May 2021 17:31:37 -0400
Subject: [PATCH 07/23] Update function viz to use gausian connection function

---
 hnn_core/cell.py | 15 +++++++++------
 hnn_core/viz.py  | 10 +++-------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/hnn_core/cell.py b/hnn_core/cell.py
index d910e4c38..e6d883c79 100644
--- a/hnn_core/cell.py
+++ b/hnn_core/cell.py
@@ -52,16 +52,18 @@ def _calculate_gaussian(x_val, height, lamtha):
     return x_height
 
 
-def _get_gaussian_connection(nc_dict, target_pos):
+def _get_gaussian_connection(src_pos, target_pos, nc_dict):
     """Calculate distance dependent connection properties.
 
     Parameters
     ----------
+    src_pos : float
+        Position of source cell.
+    target_pos : float
+        Position of target cell.
     nc_dict : dict
         Dictionary with keys: pos_src, A_weight, A_delay, lamtha
         Defines the connection parameters
-    target_pos : float
-        Position of target cell.
 
     Returns
     -------
@@ -74,8 +76,8 @@ def _get_gaussian_connection(nc_dict, target_pos):
     -----
     Distance in xy plane is used for gaussian decay.
     """
-    x_dist = target_pos[0] - nc_dict['pos_src'][0]
-    y_dist = target_pos[1] - nc_dict['pos_src'][1]
+    x_dist = target_pos[0] - src_pos[0]
+    y_dist = target_pos[1] - src_pos[1]
     cell_dist = np.sqrt(x_dist**2 + y_dist**2)
 
     weight = _calculate_gaussian(
@@ -540,7 +542,8 @@ def parconnect_from_src(self, gid_presyn, nc_dict, postsyn):
 
         # set props here.
         nc.threshold = nc_dict['threshold']
-        nc.weight[0], nc.delay = _get_gaussian_connection(nc_dict, self.pos)
+        nc.weight[0], nc.delay = _get_gaussian_connection(
+            nc_dict['pos_src'], self.pos, nc_dict)
 
         return nc
 
diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 75f536537..528d1f194 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -577,7 +577,7 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
     net : Instance of Network object
         The Network object
     conn_idx : int
-        Index of _Connectivity object to be visualized
+        Index of connection to be visualized
         from `net.connectivity`
     ax : instance of Axes3D
         Matplotlib 3D axis
@@ -591,6 +591,7 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
     """
     import matplotlib.pyplot as plt
     from .network import Network
+    from .cell import _get_gaussian_connection
 
     if not isinstance(net, Network):
         raise TypeError('conn must be instance of _Connectivity')
@@ -617,12 +618,7 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
             target_pos = target_type_pos[target_idx]
 
             # Identical calculation used in Cell.par_connect_from_src()
-            dx = src_pos[0] - target_pos[0]
-            dy = src_pos[1] - target_pos[1]
-            d = np.sqrt(dx**2 + dy**2)
-
-            weight = nc_dict['A_weight'] * \
-                np.exp(-(d**2) / (nc_dict['lamtha']**2))
+            weight, _ = _get_gaussian_connection(src_pos, target_pos, nc_dict)
 
             connectivity_matrix[src_idx, target_idx] = weight
 

From 21ab5397c683aa7630b81d217a0bf97298bc9df8 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 27 May 2021 17:35:09 -0400
Subject: [PATCH 08/23] doc fix

---
 hnn_core/cell.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hnn_core/cell.py b/hnn_core/cell.py
index e6d883c79..cf153ec1b 100644
--- a/hnn_core/cell.py
+++ b/hnn_core/cell.py
@@ -26,7 +26,7 @@ def _get_cos_theta(p_secs, sec_name_apical):
 
 
 def _calculate_gaussian(x_val, height, lamtha):
-    """Return height of gaussian at x_val.and
+    """Return height of gaussian at x_val.
 
     Parameters
     ----------

From 9a60eb8e919592449c9e3f61964d29e321880781 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 27 May 2021 18:12:09 -0400
Subject: [PATCH 09/23] Fix delay calculation

---
 hnn_core/cell.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hnn_core/cell.py b/hnn_core/cell.py
index cf153ec1b..f5464e1be 100644
--- a/hnn_core/cell.py
+++ b/hnn_core/cell.py
@@ -82,8 +82,8 @@ def _get_gaussian_connection(src_pos, target_pos, nc_dict):
 
     weight = _calculate_gaussian(
         cell_dist, nc_dict['A_weight'], nc_dict['lamtha'])
-    delay = _calculate_gaussian(
-        cell_dist, nc_dict['A_delay'], nc_dict['lamtha'])
+    delay = nc_dict['A_delay'] / _calculate_gaussian(
+        cell_dist, 1, nc_dict['lamtha'])
     return weight, delay
 
 

From c63747865b18e2898fada22edb81f2efd36fa854 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 27 May 2021 21:11:22 -0400
Subject: [PATCH 10/23] Fix type checks

---
 hnn_core/viz.py | 60 +++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 56 insertions(+), 4 deletions(-)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 528d1f194..872b03542 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -5,6 +5,7 @@
 
 import numpy as np
 from itertools import cycle
+from .externals.mne import _validate_type
 
 
 def _get_plot_data(dpl, layer, tmin, tmax):
@@ -593,8 +594,8 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
     from .network import Network
     from .cell import _get_gaussian_connection
 
-    if not isinstance(net, Network):
-        raise TypeError('conn must be instance of _Connectivity')
+    _validate_type(net, Network, 'net', 'Network')
+    _validate_type(conn_idx, int, 'conn_idx', 'int')
     if ax is None:
         _, ax = plt.subplots(1, 1)
 
@@ -657,8 +658,7 @@ def plot_connectivity_matrix(conn, ax=None, show=True):
     import matplotlib.pyplot as plt
     from.network import _Connectivity
 
-    if not isinstance(conn, _Connectivity):
-        raise TypeError('conn must be instance of _Connectivity')
+    _validate_type(conn, _Connectivity, 'conn', '_Connectivity')
     if ax is None:
         _, ax = plt.subplots(1, 1)
 
@@ -680,5 +680,57 @@ def plot_connectivity_matrix(conn, ax=None, show=True):
     ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
                  f"({conn['loc']}, {conn['receptor']})")
 
+    plt_show(show)
+    return ax.get_figure()
+
+
+def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
+    """Plot synaptic weight
+
+    Parameters
+    ----------
+    net : Instance of Network object
+        The Network object
+    conn_idx : int
+        Index of connection to be visualized
+        from `net.connectivity`
+    gid : int
+        Each cell in a network is uniquely identified by it's "global ID": GID.
+    ax : instance of Axes3D
+        Matplotlib 3D axis
+    show : bool
+        If True, show the plot
+
+    Returns
+    -------
+    fig : instance of matplotlib Figure
+        The matplotlib figure handle.
+    """
+    import matplotlib.pyplot as plt
+    from .network import Network
+    from .cell import _get_gaussian_connection
+
+    _validate_type(net, Network, 'net', 'Network')
+    _validate_type(conn_idx, int, 'conn_idx', 'int')
+    _validate_type(gid, int, 'gid', 'int')
+    if ax is None:
+        _, ax = plt.subplots(1, 1)
+
+    # Load objects for distance calculation
+    conn = net.connectivity[conn_idx]
+    nc_dict = conn['nc_dict']
+    src_type = conn['src_type']
+    target_type = conn['target_type']
+    src_type_pos = net.pos_dict[src_type]
+    target_type_pos = net.pos_dict[target_type]
+
+    # Assumes min/max values occur in the first/last pos_dict items.
+
+    src_range = np.array(conn['src_range'])
+    target_range = np.array(conn['target_range'])
+    connectivity_matrix = np.zeros((len(src_range), len(target_range)))
+
+
+
     plt_show(show)
     return ax.get_figure()

From cc56dfa622c91917913a513cdd2fa3ffc0007e3b Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 27 May 2021 22:26:15 -0400
Subject: [PATCH 11/23] WIP: Start single gid connectivity plot code

---
 hnn_core/viz.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 872b03542..2cee89b55 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -724,13 +724,15 @@ def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
     src_type_pos = net.pos_dict[src_type]
     target_type_pos = net.pos_dict[target_type]
 
-    # Assumes min/max values occur in the first/last pos_dict items.
-
+    # Assumes max value occurs in the last pos_dict items.
     src_range = np.array(conn['src_range'])
     target_range = np.array(conn['target_range'])
-    connectivity_matrix = np.zeros((len(src_range), len(target_range)))
+    connectivity_matrix = np.zeros((target_type_pos[-1][1],
+                                    (target_type_pos[-1][0])))
 
+    # src_idx = np.where()
 
+    # conn['gid_pairs']
 
-    plt_show(show)
-    return ax.get_figure()
+    # plt_show(show)
+    # return ax.get_figure()

From ceb1cfebb8fa6510e9e2b4d0086d9806cef19901 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Wed, 2 Jun 2021 17:02:31 -0400
Subject: [PATCH 12/23] Add cell weight connectivity plot

---
 examples/plot_connectivity.py | 15 ++++++++-----
 hnn_core/viz.py               | 41 +++++++++++++++++++++++++----------
 2 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index 640e76de0..806809a01 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -39,15 +39,18 @@
 # reflect the canonical neocortical microcircuit. ``net.connectivity``
 # is a list of dictionaries which detail every cell-cell, and drive-cell
 # connection. The weights of these connections can be visualized with
-# :func:`~hnn_core.viz.plot_connectivity_weights`
-from hnn_core.viz import plot_connectivity_weights
+# :func:`~hnn_core.viz.plot_connectivity_weights` as well as
+# :func:`~hnn_core.viz.plot_cell_connectivity`
+from hnn_core.viz import plot_connectivity_weights, plot_cell_connectivity
 print(len(net_erp.connectivity))
 
-print(net_erp.connectivity[15])
-plot_connectivity_weights(net_erp, conn_idx=15)
+conn_idx = 15
+print(net_erp.connectivity[conn_idx])
+plot_connectivity_weights(net_erp, conn_idx)
 
-print(net_erp.connectivity[20])
-plot_connectivity_weights(net_erp, conn_idx=20)
+conn_idx, gid_idx = 20, 11
+src_gid = net_erp.connectivity[conn_idx]['src_range'][gid_idx]
+fig, ax = plot_cell_connectivity(net_erp, conn_idx, src_gid)
 
 ###############################################################################
 # Data recorded during simulations are stored under
diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 2cee89b55..b9bbd36d2 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -684,8 +684,8 @@ def plot_connectivity_matrix(conn, ax=None, show=True):
     return ax.get_figure()
 
 
-def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
-    """Plot synaptic weight
+def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, show=True):
+    """Plot synaptic weight of connections from a src_gid.
 
     Parameters
     ----------
@@ -694,7 +694,7 @@ def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
     conn_idx : int
         Index of connection to be visualized
         from `net.connectivity`
-    gid : int
+    src_gid : int
         Each cell in a network is uniquely identified by it's "global ID": GID.
     ax : instance of Axes3D
         Matplotlib 3D axis
@@ -705,6 +705,8 @@ def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
     -------
     fig : instance of matplotlib Figure
         The matplotlib figure handle.
+    im : Instance of matplotlib AxesImage
+        The matplotlib AxesImage handle.
     """
     import matplotlib.pyplot as plt
     from .network import Network
@@ -712,7 +714,7 @@ def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
 
     _validate_type(net, Network, 'net', 'Network')
     _validate_type(conn_idx, int, 'conn_idx', 'int')
-    _validate_type(gid, int, 'gid', 'int')
+    _validate_type(src_gid, int, 'src_gid', 'int')
     if ax is None:
         _, ax = plt.subplots(1, 1)
 
@@ -724,15 +726,32 @@ def plot_cell_connectivity(net, conn_idx, gid, ax=None, show=True):
     src_type_pos = net.pos_dict[src_type]
     target_type_pos = net.pos_dict[target_type]
 
-    # Assumes max value occurs in the last pos_dict items.
     src_range = np.array(conn['src_range'])
     target_range = np.array(conn['target_range'])
-    connectivity_matrix = np.zeros((target_type_pos[-1][1],
-                                    (target_type_pos[-1][0])))
 
-    # src_idx = np.where()
+    # Extract indeces to get position in network
+    # Index in gid range aligns with net.pos_dict
+    target_src_pair = conn['gid_pairs'][src_gid]
+    target_indeces = np.where(np.in1d(target_range, target_src_pair))[0]
 
-    # conn['gid_pairs']
+    src_idx = np.where(src_range == src_gid)[0][0]
+    src_pos = src_type_pos[src_idx]
 
-    # plt_show(show)
-    # return ax.get_figure()
+    weights, x_pos, y_pos = list(), list(), list()
+    for target_idx in target_indeces:
+        target_pos = target_type_pos[target_idx]
+        x_pos.append(target_pos[0])
+        y_pos.append(target_pos[1])
+        weight, _ = _get_gaussian_connection(src_pos, target_pos, nc_dict)
+        weights.append(weight)
+
+    ax.scatter(x_pos, y_pos, c=weights)
+
+    ax.scatter(src_pos[0], src_pos[1], color='red', s=100)
+    ax.set_ylabel('Y Position')
+    ax.set_xlabel('X Position')
+    ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
+                 f"({conn['loc']}, {conn['receptor']})")
+
+    plt_show(show)
+    return ax.get_figure(), ax

From 5e9184284e5ba0fbf90a5476a59d437cd3f7fde6 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Wed, 2 Jun 2021 17:14:26 -0400
Subject: [PATCH 13/23] Better title

---
 hnn_core/viz.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index b9bbd36d2..c6750e38a 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -750,8 +750,8 @@ def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, show=True):
     ax.scatter(src_pos[0], src_pos[1], color='red', s=100)
     ax.set_ylabel('Y Position')
     ax.set_xlabel('X Position')
-    ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
-                 f"({conn['loc']}, {conn['receptor']})")
+    ax.set_title(f"{conn['src_type']} (gid={src_gid}) -> {conn['target_type']}"
+                 f" ({conn['loc']}, {conn['receptor']})")
 
     plt_show(show)
     return ax.get_figure(), ax

From 69066a77ff1791bc17846049da492a4732c52847 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 3 Jun 2021 21:08:28 -0400
Subject: [PATCH 14/23] Remove redunant function

---
 examples/plot_connectivity.py | 19 ++++++-----
 hnn_core/network.py           | 21 +-----------
 hnn_core/viz.py               | 60 +++++++----------------------------
 3 files changed, 21 insertions(+), 79 deletions(-)

diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index 806809a01..ca3aa41d4 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -41,14 +41,14 @@
 # connection. The weights of these connections can be visualized with
 # :func:`~hnn_core.viz.plot_connectivity_weights` as well as
 # :func:`~hnn_core.viz.plot_cell_connectivity`
-from hnn_core.viz import plot_connectivity_weights, plot_cell_connectivity
+from hnn_core.viz import plot_connectivity_matrix, plot_cell_connectivity
 print(len(net_erp.connectivity))
 
-conn_idx = 15
+conn_idx = 20
 print(net_erp.connectivity[conn_idx])
-plot_connectivity_weights(net_erp, conn_idx)
+plot_connectivity_matrix(net_erp, conn_idx)
 
-conn_idx, gid_idx = 20, 11
+gid_idx = 11
 src_gid = net_erp.connectivity[conn_idx]['src_range'][gid_idx]
 fig, ax = plot_cell_connectivity(net_erp, conn_idx, src_gid)
 
@@ -99,9 +99,7 @@
 # activity is visible as vertical lines where several cells fire simultaneously
 # We can additionally use the ``probability``. argument to create a sparse
 # connectivity pattern instead of all-to-all. Let's try creating the same
-# network with a 10% chance of cells connecting to each other. The resulting
-# connectivity pattern can also be visualized with
-# ``net.connectivity[idx].plot()``
+# network with a 10% chance of cells connecting to each other.
 probability = 0.1
 net_sparse = default_network(params, add_drives_from_params=True)
 net_sparse.clear_connectivity()
@@ -125,9 +123,10 @@
 dpl_sparse = simulate_dipole(net_sparse, n_trials=1)
 net_sparse.cell_response.plot_spikes_raster()
 
-net_sparse.connectivity[-2].plot()
-net_sparse.connectivity[-1].plot()
-
+# Get index of most recently added connection
+conn_idx = len(net_sparse.connectivity)
+plot_connectivity_matrix(net_sparse, conn_idx, show_weight=False)
+plot_connectivity_matrix(net_sparse, conn_idx - 1, show_weight=False)
 
 ###############################################################################
 # Using the sparse connectivity pattern produced a lot more spiking in
diff --git a/hnn_core/network.py b/hnn_core/network.py
index cb6ed0634..148ed1507 100644
--- a/hnn_core/network.py
+++ b/hnn_core/network.py
@@ -17,7 +17,7 @@
 from .cells_default import pyramidal, basket
 from .cell_response import CellResponse
 from .params import _long_name, _short_name
-from .viz import plot_cells, plot_connectivity_matrix
+from .viz import plot_cells
 from .externals.mne import _validate_type, _check_option
 
 
@@ -1268,25 +1268,6 @@ def __repr__(self):
 
         return entr
 
-    def plot(self, ax=None, show=True):
-        """Plot connectivity matrix for instance of _Connectivity object.
-
-        Parameters
-        ----------
-        ax : instance of matplotlib Axes3D | None
-            An axis object from matplotlib. If None,
-            a new figure is created.
-        show : bool
-            If True, show the figure.
-
-        Returns
-        -------
-        fig : instance of matplotlib Figure
-            The matplotlib figure handle.
-        """
-
-        return plot_connectivity_matrix(self, ax=ax, show=show)
-
 
 class _NetworkDrive(dict):
     """A class for containing the parameters of external drives
diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index c6750e38a..eda784633 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -570,7 +570,8 @@ def plot_cell_morphology(cell, ax, show=True):
     return ax
 
 
-def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
+def plot_connectivity_matrix(net, conn_idx, show_weight=True,
+                             ax=None, show=True):
     """Plot connectivity matrix with color bar for synaptic weights
 
     Parameters
@@ -580,6 +581,9 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
     conn_idx : int
         Index of connection to be visualized
         from `net.connectivity`
+    show_weight : bool
+        If True, visualize connectivity weights as gradient.
+        If False, each connection is visualized with a black square.
     ax : instance of Axes3D
         Matplotlib 3D axis
     show : bool
@@ -596,6 +600,7 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
 
     _validate_type(net, Network, 'net', 'Network')
     _validate_type(conn_idx, int, 'conn_idx', 'int')
+    _validate_type(show_weight, bool, 'show_weight', 'bool')
     if ax is None:
         _, ax = plt.subplots(1, 1)
 
@@ -619,7 +624,11 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
             target_pos = target_type_pos[target_idx]
 
             # Identical calculation used in Cell.par_connect_from_src()
-            weight, _ = _get_gaussian_connection(src_pos, target_pos, nc_dict)
+            if show_weight:
+                weight, _ = _get_gaussian_connection(
+                    src_pos, target_pos, nc_dict)
+            else:
+                weight = 1.0
 
             connectivity_matrix[src_idx, target_idx] = weight
 
@@ -637,53 +646,6 @@ def plot_connectivity_weights(net, conn_idx, ax=None, show=True):
     return ax.get_figure()
 
 
-def plot_connectivity_matrix(conn, ax=None, show=True):
-    """Plot connectivity matrix for instance of _Connectivity object.
-
-    Parameters
-    ----------
-    conn : Instance of _Connectivity object
-        The _Connectivity object
-    ax : instance of Axes3D
-        Matplotlib 3D axis
-    show : bool
-        If True, show the plot
-
-    Returns
-    -------
-    fig : instance of matplotlib Figure
-        The matplotlib figure handle.
-
-    """
-    import matplotlib.pyplot as plt
-    from.network import _Connectivity
-
-    _validate_type(conn, _Connectivity, 'conn', '_Connectivity')
-    if ax is None:
-        _, ax = plt.subplots(1, 1)
-
-    src_range = np.array(conn['src_range'])
-    target_range = np.array(conn['target_range'])
-    connectivity_matrix = np.zeros((len(src_range), len(target_range)))
-    for src_gid, target_src_pair in conn['gid_pairs'].items():
-        src_idx = np.where(src_range == src_gid)[0][0]
-        target_indeces = np.in1d(target_range, target_src_pair)
-        connectivity_matrix[src_idx, :] = target_indeces
-
-    ax.imshow(connectivity_matrix, cmap='Greys', interpolation='none')
-    ax.set_xlabel(f"{conn['target_type']} target gids "
-                  f"({target_range[0]}-{target_range[-1]})")
-    ax.set_xticklabels(list())
-    ax.set_ylabel(f"{conn['src_type']} source gids "
-                  f"({src_range[0]}-{src_range[-1]})")
-    ax.set_yticklabels(list())
-    ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
-                 f"({conn['loc']}, {conn['receptor']})")
-
-    plt_show(show)
-    return ax.get_figure()
-
-
 def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, show=True):
     """Plot synaptic weight of connections from a src_gid.
 

From 2f05e5e63510c07c5cb5ad14f805a61559078245 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 3 Jun 2021 21:20:18 -0400
Subject: [PATCH 15/23] Add simple type checks for plotting functions

---
 hnn_core/tests/test_viz.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/hnn_core/tests/test_viz.py b/hnn_core/tests/test_viz.py
index 2f234c64a..fbb3c11e7 100644
--- a/hnn_core/tests/test_viz.py
+++ b/hnn_core/tests/test_viz.py
@@ -7,6 +7,7 @@
 import hnn_core
 from hnn_core import read_params, default_network
 from hnn_core.viz import plot_cells, plot_dipole, plot_psd, plot_tfr_morlet
+from hnn_core.viz import plot_connectivity_matrix, plot_cell_connectivity
 from hnn_core.dipole import simulate_dipole
 
 matplotlib.use('agg')
@@ -24,6 +25,26 @@ def test_network_visualization():
     ax = net.cell_types['L2_pyramidal'].plot_morphology()
     assert len(ax.lines) == 8
 
+    conn_idx = 0
+    with pytest.raises(TypeError, match='net must be an instance of'):
+        plot_connectivity_matrix('blah', conn_idx, show_weight=False)
+
+    with pytest.raises(TypeError, match='conn_idx must be an instance of'):
+        plot_connectivity_matrix(net, 'blah', show_weight=False)
+
+    with pytest.raises(TypeError, match='show_weight must be an instance of'):
+        plot_connectivity_matrix(net, conn_idx, show_weight='blah')
+
+    src_gid = 5
+    with pytest.raises(TypeError, match='net must be an instance of'):
+        plot_cell_connectivity('blah', conn_idx, src_gid=src_gid)
+
+    with pytest.raises(TypeError, match='conn_idx must be an instance of'):
+        plot_cell_connectivity(net, 'blah', src_gid=src_gid)
+
+    with pytest.raises(TypeError, match='src_gid must be an instance of'):
+        plot_cell_connectivity(net, conn_idx, src_gid='blah')
+
 
 def test_dipole_visualization():
     """Test dipole visualisations."""

From 498377ffbaad45fd914dd9cb07775caa1cac0e4d Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Thu, 3 Jun 2021 21:45:58 -0400
Subject: [PATCH 16/23] WIP: Start adding colorbar options

---
 hnn_core/viz.py | 38 +++++++++++++++++++++++++++++++-------
 1 file changed, 31 insertions(+), 7 deletions(-)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index eda784633..6a50e4c3a 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -571,7 +571,7 @@ def plot_cell_morphology(cell, ax, show=True):
 
 
 def plot_connectivity_matrix(net, conn_idx, show_weight=True,
-                             ax=None, show=True):
+                             colorbar=True, ax=None, show=True):
     """Plot connectivity matrix with color bar for synaptic weights
 
     Parameters
@@ -595,6 +595,7 @@ def plot_connectivity_matrix(net, conn_idx, show_weight=True,
         The matplotlib figure handle.
     """
     import matplotlib.pyplot as plt
+    from matplotlib.ticker import ScalarFormatter
     from .network import Network
     from .cell import _get_gaussian_connection
 
@@ -632,7 +633,19 @@ def plot_connectivity_matrix(net, conn_idx, show_weight=True,
 
             connectivity_matrix[src_idx, target_idx] = weight
 
-    ax.imshow(connectivity_matrix, cmap='Greys', interpolation='none')
+    im = ax.imshow(connectivity_matrix, cmap='Greys', interpolation='none')
+
+    ax.set_xlabel('Time (ms)')
+    ax.set_ylabel('Frequency (Hz)')
+
+    if colorbar:
+        fig = ax.get_figure()
+        xfmt = ScalarFormatter()
+        xfmt.set_powerlimits((-2, 2))
+        cbar = fig.colorbar(im, ax=ax, format=xfmt)
+        cbar.ax.yaxis.set_ticks_position('right')
+        cbar.ax.set_ylabel('Weight', rotation=-90, va="bottom")
+
     ax.set_xlabel(f"{conn['target_type']} target gids "
                   f"({target_range[0]}-{target_range[-1]})")
     ax.set_xticklabels(list())
@@ -642,11 +655,13 @@ def plot_connectivity_matrix(net, conn_idx, show_weight=True,
     ax.set_title(f"{conn['src_type']} -> {conn['target_type']} "
                  f"({conn['loc']}, {conn['receptor']})")
 
+    plt.tight_layout()
     plt_show(show)
     return ax.get_figure()
 
 
-def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, show=True):
+def plot_cell_connectivity(net, conn_idx, src_gid, colorbar=True,
+                           ax=None, show=True):
     """Plot synaptic weight of connections from a src_gid.
 
     Parameters
@@ -667,12 +682,12 @@ def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, show=True):
     -------
     fig : instance of matplotlib Figure
         The matplotlib figure handle.
-    im : Instance of matplotlib AxesImage
-        The matplotlib AxesImage handle.
+
     """
     import matplotlib.pyplot as plt
     from .network import Network
     from .cell import _get_gaussian_connection
+    from matplotlib.ticker import ScalarFormatter
 
     _validate_type(net, Network, 'net', 'Network')
     _validate_type(conn_idx, int, 'conn_idx', 'int')
@@ -707,13 +722,22 @@ def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, show=True):
         weight, _ = _get_gaussian_connection(src_pos, target_pos, nc_dict)
         weights.append(weight)
 
-    ax.scatter(x_pos, y_pos, c=weights)
+    im = ax.scatter(x_pos, y_pos, c=weights)
 
     ax.scatter(src_pos[0], src_pos[1], color='red', s=100)
     ax.set_ylabel('Y Position')
     ax.set_xlabel('X Position')
-    ax.set_title(f"{conn['src_type']} (gid={src_gid}) -> {conn['target_type']}"
+    ax.set_title(f"{conn['src_type']}-> {conn['target_type']}"
                  f" ({conn['loc']}, {conn['receptor']})")
 
+    if colorbar:
+        fig = ax.get_figure()
+        xfmt = ScalarFormatter()
+        xfmt.set_powerlimits((-2, 2))
+        cbar = fig.colorbar(im, ax=ax, format=xfmt)
+        cbar.ax.yaxis.set_ticks_position('right')
+        cbar.ax.set_ylabel('Weight', rotation=-90, va="bottom")
+
+    plt.tight_layout()
     plt_show(show)
     return ax.get_figure(), ax

From b295434d17ced23cb022e7b49bf23a8e3bff95b0 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 11:42:05 -0400
Subject: [PATCH 17/23] Better viz and docs

---
 hnn_core/viz.py | 59 +++++++++++++++++++++++++++++++++++++------------
 1 file changed, 45 insertions(+), 14 deletions(-)

diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 6a50e4c3a..4becb06f7 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -570,8 +570,9 @@ def plot_cell_morphology(cell, ax, show=True):
     return ax
 
 
-def plot_connectivity_matrix(net, conn_idx, show_weight=True,
-                             colorbar=True, ax=None, show=True):
+def plot_connectivity_matrix(net, conn_idx, ax=None, show_weight=True,
+                             colorbar=True, colormap='Greys',
+                             show=True):
     """Plot connectivity matrix with color bar for synaptic weights
 
     Parameters
@@ -581,11 +582,15 @@ def plot_connectivity_matrix(net, conn_idx, show_weight=True,
     conn_idx : int
         Index of connection to be visualized
         from `net.connectivity`
-    show_weight : bool
-        If True, visualize connectivity weights as gradient.
-        If False, each connection is visualized with a black square.
     ax : instance of Axes3D
         Matplotlib 3D axis
+    show_weight : bool
+        If True, visualize connectivity weights as gradient.
+        If False, all weights set to constant value.
+    colormap : str
+        The name of a matplotlib colormap. Default: 'Greys'
+    colorbar : bool
+        If True (default), adjust figure to include colorbar.
     show : bool
         If True, show the plot
 
@@ -633,7 +638,7 @@ def plot_connectivity_matrix(net, conn_idx, show_weight=True,
 
             connectivity_matrix[src_idx, target_idx] = weight
 
-    im = ax.imshow(connectivity_matrix, cmap='Greys', interpolation='none')
+    im = ax.imshow(connectivity_matrix, cmap=colormap, interpolation='none')
 
     ax.set_xlabel('Time (ms)')
     ax.set_ylabel('Frequency (Hz)')
@@ -660,9 +665,9 @@ def plot_connectivity_matrix(net, conn_idx, show_weight=True,
     return ax.get_figure()
 
 
-def plot_cell_connectivity(net, conn_idx, src_gid, colorbar=True,
-                           ax=None, show=True):
-    """Plot synaptic weight of connections from a src_gid.
+def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, colorbar=True,
+                           colormap='viridis', show=True):
+    """Plot synaptic weight of connections originating from src_gid.
 
     Parameters
     ----------
@@ -675,6 +680,10 @@ def plot_cell_connectivity(net, conn_idx, src_gid, colorbar=True,
         Each cell in a network is uniquely identified by it's "global ID": GID.
     ax : instance of Axes3D
         Matplotlib 3D axis
+    colormap : str
+        The name of a matplotlib colormap. Default: 'viridis'
+    colorbar : bool
+        If True (default), adjust figure to include colorbar.
     show : bool
         If True, show the plot
 
@@ -683,6 +692,15 @@ def plot_cell_connectivity(net, conn_idx, src_gid, colorbar=True,
     fig : instance of matplotlib Figure
         The matplotlib figure handle.
 
+    Notes
+    -----
+    Target cells will be determined by the connection class given by
+    net.connectivity[conn_idx].
+    If the target cell is not connected to src_gid, it will appear as a
+    smaller black circle.
+    src_gid is plotted as a red circle. src_gid will not be plotted if
+    the connection corresponds to a drive, ex: poisson, bursty, etc.
+
     """
     import matplotlib.pyplot as plt
     from .network import Network
@@ -704,6 +722,11 @@ def plot_cell_connectivity(net, conn_idx, src_gid, colorbar=True,
     target_type_pos = net.pos_dict[target_type]
 
     src_range = np.array(conn['src_range'])
+    if src_gid not in src_range:
+        raise ValueError(f'src_gid not in the src type range of {src_type} '
+                         f'gids. Valid gids include {src_range[0]} -> '
+                         f'{src_range[-1]}')
+
     target_range = np.array(conn['target_range'])
 
     # Extract indeces to get position in network
@@ -714,17 +737,25 @@ def plot_cell_connectivity(net, conn_idx, src_gid, colorbar=True,
     src_idx = np.where(src_range == src_gid)[0][0]
     src_pos = src_type_pos[src_idx]
 
-    weights, x_pos, y_pos = list(), list(), list()
+    # Aggregate positions and weight of each connected target
+    weights, target_x_pos, target_y_pos = list(), list(), list()
     for target_idx in target_indeces:
         target_pos = target_type_pos[target_idx]
-        x_pos.append(target_pos[0])
-        y_pos.append(target_pos[1])
+        target_x_pos.append(target_pos[0])
+        target_y_pos.append(target_pos[1])
         weight, _ = _get_gaussian_connection(src_pos, target_pos, nc_dict)
         weights.append(weight)
 
-    im = ax.scatter(x_pos, y_pos, c=weights)
+    im = ax.scatter(target_x_pos, target_y_pos, c=weights, cmap=colormap)
+
+    # Gather positions of all gids in target_type.
+    x_pos = [target_type_pos[idx][0] for idx in range(len(target_type_pos))]
+    y_pos = [target_type_pos[idx][1] for idx in range(len(target_type_pos))]
+    ax.scatter(x_pos, y_pos, color='k', zorder=-1, s=4)
 
-    ax.scatter(src_pos[0], src_pos[1], color='red', s=100)
+    # Only plot src_gid if proper cell type.
+    if src_type in net.cell_types:
+        ax.scatter(src_pos[0], src_pos[1], color='red', s=100)
     ax.set_ylabel('Y Position')
     ax.set_xlabel('X Position')
     ax.set_title(f"{conn['src_type']}-> {conn['target_type']}"

From cf7584c5e4da378ecdd74e274f01acef0d43b9d5 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 11:42:23 -0400
Subject: [PATCH 18/23] Smoke tests

---
 hnn_core/tests/test_viz.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/hnn_core/tests/test_viz.py b/hnn_core/tests/test_viz.py
index fbb3c11e7..6c27db717 100644
--- a/hnn_core/tests/test_viz.py
+++ b/hnn_core/tests/test_viz.py
@@ -26,6 +26,7 @@ def test_network_visualization():
     assert len(ax.lines) == 8
 
     conn_idx = 0
+    plot_connectivity_matrix(net, conn_idx, show=False)
     with pytest.raises(TypeError, match='net must be an instance of'):
         plot_connectivity_matrix('blah', conn_idx, show_weight=False)
 
@@ -36,15 +37,19 @@ def test_network_visualization():
         plot_connectivity_matrix(net, conn_idx, show_weight='blah')
 
     src_gid = 5
+    plot_cell_connectivity(net, conn_idx, src_gid, show=False)
     with pytest.raises(TypeError, match='net must be an instance of'):
         plot_cell_connectivity('blah', conn_idx, src_gid=src_gid)
 
     with pytest.raises(TypeError, match='conn_idx must be an instance of'):
-        plot_cell_connectivity(net, 'blah', src_gid=src_gid)
+        plot_cell_connectivity(net, 'blah', src_gid)
 
     with pytest.raises(TypeError, match='src_gid must be an instance of'):
         plot_cell_connectivity(net, conn_idx, src_gid='blah')
 
+    with pytest.raises(ValueError, match='src_gid not in the'):
+        plot_cell_connectivity(net, conn_idx, src_gid=-1)
+
 
 def test_dipole_visualization():
     """Test dipole visualisations."""

From 4f952119adee77d0282738954403b7a0970a384d Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 12:01:53 -0400
Subject: [PATCH 19/23] Update examples

---
 examples/plot_connectivity.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index ca3aa41d4..8f15aa0bd 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -123,10 +123,16 @@
 dpl_sparse = simulate_dipole(net_sparse, n_trials=1)
 net_sparse.cell_response.plot_spikes_raster()
 
-# Get index of most recently added connection
-conn_idx = len(net_sparse.connectivity)
-plot_connectivity_matrix(net_sparse, conn_idx, show_weight=False)
-plot_connectivity_matrix(net_sparse, conn_idx - 1, show_weight=False)
+# Get index of most recently added connection, and a src_gid in src_range.
+conn_idx, gid_idx = len(net_sparse.connectivity) - 1, 5
+src_gid = net_erp.connectivity[conn_idx]['src_range'][gid_idx]
+plot_connectivity_matrix(net_sparse, conn_idx)
+plot_cell_connectivity(net_sparse, conn_idx, src_gid)
+
+conn_idx, gid_idx = len(net_sparse.connectivity) - 2, 5
+src_gid = net_erp.connectivity[conn_idx]['src_range'][gid_idx]
+plot_connectivity_matrix(net_sparse, conn_idx)
+plot_cell_connectivity(net_sparse, conn_idx, src_gid)
 
 ###############################################################################
 # Using the sparse connectivity pattern produced a lot more spiking in

From 0633e7ffe88c6ecdb3476c15995fed7118df8c45 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 12:14:43 -0400
Subject: [PATCH 20/23] Fix example, update what_new.rst

---
 doc/whats_new.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index de686b49e..9ad3bf26a 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -24,6 +24,8 @@ Changelog
 
 - Add probability argument to :func:`~hnn_core.Network.add_connection`. Connectivity patterns can also be visualized with :func:`~hnn_core.viz.plot_connectivity_matrix`, by `Nick Tolley`_ in `#318 <https://github.com/jonescompneurolab/hnn-core/pull/318>`_
 
+- Add function to visualize connections originating from individual cells :func:`~hnn_core.viz.plot_cell_connectivity`, by `Nick Tolley`_ in `#339 <https://github.com/jonescompneurolab/hnn-core/pull/339>`_
+
 Bug
 ~~~
 

From 40d00849604ddbc7f3fe869351529cc78406080c Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 12:39:14 -0400
Subject: [PATCH 21/23] example fix

---
 examples/plot_connectivity.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index 8f15aa0bd..c2b90f258 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -125,12 +125,12 @@
 
 # Get index of most recently added connection, and a src_gid in src_range.
 conn_idx, gid_idx = len(net_sparse.connectivity) - 1, 5
-src_gid = net_erp.connectivity[conn_idx]['src_range'][gid_idx]
+src_gid = net_sparse.connectivity[conn_idx]['src_range'][gid_idx]
 plot_connectivity_matrix(net_sparse, conn_idx)
 plot_cell_connectivity(net_sparse, conn_idx, src_gid)
 
 conn_idx, gid_idx = len(net_sparse.connectivity) - 2, 5
-src_gid = net_erp.connectivity[conn_idx]['src_range'][gid_idx]
+src_gid = net_sparse.connectivity[conn_idx]['src_range'][gid_idx]
 plot_connectivity_matrix(net_sparse, conn_idx)
 plot_cell_connectivity(net_sparse, conn_idx, src_gid)
 

From 3e5981ac142d5fa293d2ba029254ba6ec2f035aa Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 18:48:44 -0400
Subject: [PATCH 22/23] Update docs, modify plot markers

---
 doc/whats_new.rst             | 4 ++--
 examples/plot_connectivity.py | 2 +-
 hnn_core/viz.py               | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 9ad3bf26a..9cb5ef4a2 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -24,8 +24,6 @@ Changelog
 
 - Add probability argument to :func:`~hnn_core.Network.add_connection`. Connectivity patterns can also be visualized with :func:`~hnn_core.viz.plot_connectivity_matrix`, by `Nick Tolley`_ in `#318 <https://github.com/jonescompneurolab/hnn-core/pull/318>`_
 
-- Add function to visualize connections originating from individual cells :func:`~hnn_core.viz.plot_cell_connectivity`, by `Nick Tolley`_ in `#339 <https://github.com/jonescompneurolab/hnn-core/pull/339>`_
-
 Bug
 ~~~
 
@@ -45,6 +43,8 @@ API
 
 - New API for network creation. The default network is now created with ``net = default_network(params)``, by `Nick Tolley`_ in `#318 <https://github.com/jonescompneurolab/hnn-core/pull/318>`_
 
+- Add API for visualizing connections originating from individual cells :func:`~hnn_core.viz.plot_cell_connectivity`, by `Nick Tolley`_ in `#339 <https://github.com/jonescompneurolab/hnn-core/pull/339>`_
+
 .. _0.1:
 
 0.1
diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py
index c2b90f258..29884999b 100644
--- a/examples/plot_connectivity.py
+++ b/examples/plot_connectivity.py
@@ -8,7 +8,7 @@
 
 # Author: Nick Tolley <nicholas_tolley@brown.edu>
 
-# sphinx_gallery_thumbnail_number = 1
+# sphinx_gallery_thumbnail_number = 2
 
 import os.path as op
 
diff --git a/hnn_core/viz.py b/hnn_core/viz.py
index 4becb06f7..fe1e15c07 100644
--- a/hnn_core/viz.py
+++ b/hnn_core/viz.py
@@ -746,16 +746,16 @@ def plot_cell_connectivity(net, conn_idx, src_gid, ax=None, colorbar=True,
         weight, _ = _get_gaussian_connection(src_pos, target_pos, nc_dict)
         weights.append(weight)
 
-    im = ax.scatter(target_x_pos, target_y_pos, c=weights, cmap=colormap)
+    im = ax.scatter(target_x_pos, target_y_pos, c=weights, s=50, cmap=colormap)
 
     # Gather positions of all gids in target_type.
     x_pos = [target_type_pos[idx][0] for idx in range(len(target_type_pos))]
     y_pos = [target_type_pos[idx][1] for idx in range(len(target_type_pos))]
-    ax.scatter(x_pos, y_pos, color='k', zorder=-1, s=4)
+    ax.scatter(x_pos, y_pos, color='k', marker='x', zorder=-1, s=20)
 
     # Only plot src_gid if proper cell type.
     if src_type in net.cell_types:
-        ax.scatter(src_pos[0], src_pos[1], color='red', s=100)
+        ax.scatter(src_pos[0], src_pos[1], marker='s', color='red', s=150)
     ax.set_ylabel('Y Position')
     ax.set_xlabel('X Position')
     ax.set_title(f"{conn['src_type']}-> {conn['target_type']}"

From 9d1d93c2e33d8524cbc8350313ab7929a02c2d73 Mon Sep 17 00:00:00 2001
From: Nick Tolley <nic.m.tolley@gmail.com>
Date: Fri, 4 Jun 2021 18:51:06 -0400
Subject: [PATCH 23/23] Update api.rst

---
 doc/api.rst       | 2 ++
 doc/whats_new.rst | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/doc/api.rst b/doc/api.rst
index 075bab4e1..650d19552 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -46,6 +46,8 @@ Visualization (:py:mod:`hnn_core.viz`):
    plot_cell_morphology
    plot_psd
    plot_tfr_morlet
+   plot_cell_connectivity
+   plot_connectivity_matrix
 
 Parallel backends (:py:mod:`hnn_core.parallel_backends`):
 ---------------------------------------------------------
diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 9cb5ef4a2..9ad3bf26a 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -24,6 +24,8 @@ Changelog
 
 - Add probability argument to :func:`~hnn_core.Network.add_connection`. Connectivity patterns can also be visualized with :func:`~hnn_core.viz.plot_connectivity_matrix`, by `Nick Tolley`_ in `#318 <https://github.com/jonescompneurolab/hnn-core/pull/318>`_
 
+- Add function to visualize connections originating from individual cells :func:`~hnn_core.viz.plot_cell_connectivity`, by `Nick Tolley`_ in `#339 <https://github.com/jonescompneurolab/hnn-core/pull/339>`_
+
 Bug
 ~~~
 
@@ -43,8 +45,6 @@ API
 
 - New API for network creation. The default network is now created with ``net = default_network(params)``, by `Nick Tolley`_ in `#318 <https://github.com/jonescompneurolab/hnn-core/pull/318>`_
 
-- Add API for visualizing connections originating from individual cells :func:`~hnn_core.viz.plot_cell_connectivity`, by `Nick Tolley`_ in `#339 <https://github.com/jonescompneurolab/hnn-core/pull/339>`_
-
 .. _0.1:
 
 0.1