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analysis:course-w16:week16 [2016/02/29 14:10]
mvdm [Implementing a basic co-occurrence analysis from scratch]
analysis:course-w16:week16 [2018/07/07 10:19] (current)
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 ~~DISCUSSION~~ ~~DISCUSSION~~
- 
-:!: **UNDER CONSTRUCTION,​ PLEASE DO NOT USE YET** :!: 
  
 ===== Pairwise co-occurrence ===== ===== Pairwise co-occurrence =====
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 === Setup and data loading === === Setup and data loading ===
  
-First, make sure you do a ''​git pull''​ as usual, and get the data. We'll be using session ''​R064-2015-04-22''​. You'll also need to include the ''​tasks\Alyssa-Tmaze''​ and ''​tasks\ReplayAnalysis''​ folders in your path.+First, make sure you do a ''​git pull''​ as usual, and get the data. We'll be using session ''​R064-2015-04-22''​. You'll also need to include the ''​tasks\Alyssa-Tmaze''​ and ''​tasks\Replay_Analysis''​ folders in your path.
  
 Then, we load the data: Then, we load the data:
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 ylabels = {{'​Proportion of';'​SWRs active'​},​{'​Cell pair'; 'joint probability'​},​{'​SWR coactivation';​ '​Z-score'​}};​ ylabels = {{'​Proportion of';'​SWRs active'​},​{'​Cell pair'; 'joint probability'​},​{'​SWR coactivation';​ '​Z-score'​}};​
 arms = {'​L','​R'​};​ arms = {'​L','​R'​};​
 +colors = flipud(linspecer(2));​
 location = [1 2.5]; location = [1 2.5];
  
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         ​         ​
     h(iP) = subplot(1,​3,​iP);​     h(iP) = subplot(1,​3,​iP);​
-    for iBar = 1:2+    for iBar = 1:length(arms)
     ​     ​
         bar(location(iBar),​p_data(iP,​iBar),'​FaceColor',​colors(iBar,:​),'​EdgeColor','​none'​)         bar(location(iBar),​p_data(iP,​iBar),'​FaceColor',​colors(iBar,:​),'​EdgeColor','​none'​)
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 ★ Why don't we just look at single-cell activation? Under what conditions would the results from that be the same, or different, from pairwise co-occurrence?​ ★ Why don't we just look at single-cell activation? Under what conditions would the results from that be the same, or different, from pairwise co-occurrence?​
 +
 +★ Comment on the choice of bins used in constructing the Q-matrix. It it reasonable to assume that SWR events are always 100ms in length? Modify the code to use the actual length of SWR events. Is the resampling statistic still doing the right thing in this case?
 +
 +★ Implement co-occurrence analysis on your own data.
  
 ==== Credits ==== ==== Credits ====
  
 This module was developed by [[https://​github.com/​aacarey | Alyssa Carey]]. This module was developed by [[https://​github.com/​aacarey | Alyssa Carey]].
analysis/course-w16/week16.1456773012.txt.gz · Last modified: 2018/07/07 10:19 (external edit)