# 1st July 2019
This directory contains data (1) and scripts (2, 3) relevant for the manuscript
"Individual, but not population asymmetries, are modulated by social environment 
and genotype in Drosophila melanogaster" by Versace, Caffini, Werkhoven, de Bivort.

1.Data
This directory contains data used for the analysis. 
The format of the dataset consists in the output of tracking the (x,y) position and related features (e.g. velocity, distance) of flies in a circular arena using the software Flytracker - http://www.vision.caltech.edu/Tools/FlyTracker/ -
For each video we have a trak.mat file and a feat.mat file. For instance, for a video in which we tracked the DGRP line RAL-136 (d338), with a pair of males (mm), trial 3 (t5) we had as outputs 
d338mmt5joined-feat.mat and  d338mmt5joined-track.mat

You can find the description of the output here: http://www.vision.caltech.edu/Tools/FlyTracker/documentation.html
and we report the description below 
Output:
-track.mat 	raw tracking data (e.g. position, orientation, left wing angle)
     trk.names 	     {1 x n_fields cell} names of fields in trk.data
     trk.data 	     [n_flies x n_frames x n_fields double] tracking data matrix
     trk.flags 	     [n_flags x 5 double] potential identity swaps (fly1 fly2 start_fr end_fr ambig)
-feat.mat 	features derived from tracking data (e.g. velocity, distance to wall)
     feat.names 	     {1 x n_fields cell} names of fields in feat.data
     feat.units 	     {1 x n_fields cell} units of fields in feat.data
     feat.data 	     [n_flies x n_frames x n_fields double] feature data matrix
-seg.mat 	foreground/body/wing/leg pixel locations
-JAABA 	folder suitable for JAABA processing, containing tracking and video data
-actions.mat 	list of actions annotated by user using the visualizer tool
     behs 	     {1 x n_behs cell} names of annotated actions
     bouts 	     {n_flies x n_behs cell} list of bouts for all flies and actions (start_fr end_fr certainty)

Feature description:
	individual features
'vel'    speed of fly
'ang_vel' angular velocity of fly
'min_wing_ang' mininum of left and right wing angle
'max_wing_ang' maximum of left and right wing angle
'mean_wing_length' mean of left and right wing length
'axis_ratio' major axis length divided by minor axis length
'fg_body_ratio' foreground area divided by body area
'contrast' mean gradient in image around fly
'dist_to_wall' distance to wall
	relative features
'dist_to_other' distance between the centers of the two flies
'leg_dist' minimum distance between foregrounds of the two flies
'angle_between' angle between the facing vectors of the two flies
'facing_angle' angle between facing vector and the vector towards other fly 

2_LOAD_circling - load_data_circling_index
This directory contains a MATLAB file with the instructions on how to load datasets and how to compute the circling index in a MATLAB script

3_HEATMAP - scripts_heatmap_position
This directory contains the instructions (readme_heatmap.txt) and scripts to 
(a) fix a bug in the feat files ouputted by Flytracker using the calibration files and the script feat_compute_revised.m
(b) plot the heatmap of the position and distance between partner flies in a dyad