From dcf310d8706fa91a43f8e5a15a1480325d2a4a04 Mon Sep 17 00:00:00 2001
From: ShekharNarayanan <62333171+ShekharNarayanan@users.noreply.github.com>
Date: Sat, 2 Jul 2022 13:52:29 +0200
Subject: [PATCH] Create Firing_Rates.m

---
 Shekhar/Firing_Rates.m | 75 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 Shekhar/Firing_Rates.m

diff --git a/Shekhar/Firing_Rates.m b/Shekhar/Firing_Rates.m
new file mode 100644
index 0000000..c889f0a
--- /dev/null
+++ b/Shekhar/Firing_Rates.m
@@ -0,0 +1,75 @@
+% This script visualizes the firing activity of neurons in different sleep stages per
+% treatment.
+
+
+%% Loading Data
+load('RGS_Session_1.mat')
+% load('RGS_Pyr_S1_No_Rn3.mat')
+load('Vehicle_Session_1.mat') 
+
+
+Pyr_RGS=RGS14_Session_1.Pyramidal_Cells;
+Pyr_Veh=Vehicle_Session_1.Pyramidal_Cells;
+
+
+%% Correcting for Outliers Lisa found
+
+% Loading excel sheets and collecting Neuron IDs and Wake firing rates
+% used for new threshold for groups
+Corrected_Var_RGS= table2struct(readtable('Stage_Wise_Unit_Wise_FR_Data_Both_Treatments_wexclusion.xlsx','Sheet',1));
+RGS_Useful_Data= [{{Corrected_Var_RGS(:).NeuronIDs}'} ,{[Corrected_Var_RGS.Wake]'}];
+Corrected_Var_Veh= table2struct(readtable('Stage_Wise_Unit_Wise_FR_Data_Both_Treatments_wexclusion.xlsx','Sheet',2));
+Veh_Useful_Data= [{{Corrected_Var_Veh(:).NeuronIDs}'} ,{[Corrected_Var_Veh.Wake]'}];
+
+%% Name collection for corrected Data
+% RGS
+Temp_Pyr_RGS=[]; Temp_Pyr_Veh =[];
+for i1=1:length(RGS_Useful_Data{1})
+    Names=RGS_Useful_Data{1};
+    Name=Names{i1};
+    for i2=1:length(Pyr_RGS)
+        if strcmp(Pyr_RGS(i2).WFM_Titles,Name)
+            Temp_Pyr_RGS=[Temp_Pyr_RGS; Pyr_RGS(i2)];
+        end
+    end
+       
+end
+
+%Veh
+for i1=1:length(Veh_Useful_Data{1})
+    Names=Veh_Useful_Data{1};
+    Name=Names{i1};
+    for i2=1:length(Pyr_Veh)
+        if strcmp(Pyr_Veh(i2).WFM_Titles,Name)
+            Temp_Pyr_Veh=[Temp_Pyr_Veh; Pyr_Veh(i2)];
+        end
+    end
+       
+end
+
+%% Replacing Data with Temp Data
+% doing this ^ helps us run the remaining part (relevant) of the script
+% without changing local variables
+
+Pyr_RGS= Temp_Pyr_RGS;
+Pyr_Veh= Temp_Pyr_Veh;
+
+
+% Acquiring data for the plots
+[ Pyr_RGS_RP_Data, Pyr_RGS_Unit_Wise_Data, Pyr_RGS_Session_1_Units]=FR_Analysis(Pyr_RGS);
+[ Pyr_Veh_RP_Data, Pyr_Veh_Unit_Wise_Data, Pyr_Veh_Session_1_Units]=FR_Analysis(Pyr_Veh);
+
+%% Swarm Charts ALL (per unit activity) %% Modify according to what Lisa said (Wake, NREM - NREM, REM- REM)
+
+%RGS
+figure('Name','Swarm Charts ALL RGS')
+plotSpread(Pyr_RGS_Unit_Wise_Data,'xNames',{'QW','MA','NREM','InterM','REM','Wake'},'distributionColors',{'r','g','b','y','c',[0.3 0.2 0.5]},'yLabel','Firing Rate Across Study Day')
+title('FR vs Sleep Stages: Swarm Plot-RGS14')
+ylim([0 15])
+
+% Vehicle
+figure('Name','Swarm Charts ALL Veh')
+plotSpread(Pyr_Veh_Unit_Wise_Data,'xNames',{'QW','MA','NREM','InterM','REM','Wake'},'distributionColors',{'r','g','b','y','c',[0.3 0.2 0.5]},'yLabel','Firing Rate Across Study Day')
+title('FR vs Sleep Stages: Swarm Plot- Vehicle')
+ylim([0 15])
+