Calcium_trace.py

# -*- coding: utf-8 -*-
"""
Created on Thu Apr 19 10:19:03 2018
@author: Bea
"""
'''Script for generating neuronal traces and plot them against behaviour background'''

import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.patches as patches

"""
Function that selects different beh and gives a tupla with beh and occurence of each beh
"""
def beh_select(Series):
    occurence=0
    lista = []
    for i in range (len(Series)):
        if i == len(Series)-1:
            occurence=occurence+1
            tupla=(occurence,Series.iloc[i])
            lista.append(tupla)
            
        elif Series.iloc[i] == Series.iloc[i+1]:
             occurence=occurence+1
             
        else:
            occurence=occurence+1
            tupla = (occurence,Series.iloc[i])
            lista.append(tupla)
            occurence=0
    return lista

"""
Function that creates a rectangle for each beh in behList; the each rectangle's color changes with the beh
"""
def SelectableColors(behList, ColorList, minimum, maximum, dic):
    pos = 0
    listaRect = []
    for el in behList:
        p1 = (pos, minimum)
        beh = el[1]
        width = el[0]
        pos = width + pos
        if beh in dic.keys():
            rect = patches.Rectangle (p1, width, 5, facecolor = dic.get(beh))
        else:
            for col in ColorList:
                print(str(ColorList.index(col)) + '  ' + col)
            colorIndex = int(input('insert the color number for ' + beh + ':'))
            dic.update ({beh: ColorList[colorIndex]})
            rect = patches.Rectangle(p1, width, 5, facecolor=ColorList[colorIndex])
           
        listaRect.append(rect)
    return (listaRect, dic)

"""
Function that returns a list of n colors that can be selected to do the rectangles 
"""
def GenColorList (n):
    ColorList = []
    for name, cod in matplotlib.colors.cnames.items(): 
        ColorList.append(name)
       
    return ColorList [0:n]
        
"""
Function that makes graphs
"""
def Graphing (listaColumns, lista_beh, ListColor):
    count = 0
    p = 0
    dictBehColor = {}
    Axes = []
    for el in listaColumns:
        plt.subplot (len(listaColumns), 1, count+1)
        if dictBehColor == {}:
            fig = plt.figure(figsize=(75,50))
        Axes.append(fig.add_subplot(len(listaColumns), 1, count+1))
        Axes[count].plot(el,'k',linewidth=5)
        fig.suptitle('Comparison', fontsize=100)
        plt.ylabel(el.name, fontsize = 30)
        plt.tick_params(labelsize=30)
        print(el.min())
        tuplaRectColors = SelectableColors(lista_beh, ListColor, el.min(), el.max(), dictBehColor)
        dictBehColor = tuplaRectColors[1]
        RectList = tuplaRectColors[0]
        for rect in RectList:
            Axes[count].add_patch(rect)
        count += 1
        p = p + 0.05
    plt.xlabel('Frames',  fontsize=50)
    j = 1
    for beh in dictBehColor.keys():
        legend_patch = patches.Patch(color = dictBehColor.get(beh), label = beh)
        legenda = plt.legend(handles = [legend_patch], loc=1, bbox_to_anchor=(1.1 ,p*j),  prop={'size':40})
        if j != len(dictBehColor.keys()):
            j+=1
            Axes[len(Axes) -1] = plt.gca().add_artist(legenda)
            #aggiunge di volta in volta la legenda creata sopra al grafico
        else:  
            fig.savefig('Path_to_save_figure.png',transparent=True, facecolor='white')

''' 
Import Data
'''        
Data_beh=pd.read_csv("Path_to_dataframe_with_calcium_traces.csv", sep=',')
Data_beh=Data_beh.dropna()
x = Data_beh.loc[ : ,'Frames']
beh = Data_beh.loc[:,'Beh'] 
lista_beh = beh_select(beh)
ListColor = GenColorList(150)
listMean = []  
listSeries = []
for Mean in Data_beh:
    listMean.append(Mean)
while True:
    for el in listMean:
        print (str(listMean.index(el)-1)+' ' + el)
    val = int (input('Insert Mean Number, select 0 when you have finished!'))
    if val == 0:
        break
    neuron = listMean[val+1]
#    listMean.remove (neuron)
    listSeries.append(Data_beh.loc[:,neuron])

Graphing (listSeries, lista_beh, ListColor)