I’m also trying to export graphs (Li’s ICA) out of coloc2. I tried some different approaches and I have some questions about them.
Based on this previous post, I’m also trying to use the groovy code (thanks for sharing this code!). If I understand the code correctly, it is not applying any ROI/mask in the coloc2 analysis. Could someone get me started to change the code to implement the possibility to use a ROI in the analysis? (It is the first time to use groovy).
Besides the groovy code I also tried to replot the scatterplot using the export ‘list’ function in coloc2. To plot the values I used matlab but for some reason the values in this list give an inverted y-axis. To plot I used : h=scatter(x,y,,z, ‘filled’, ‘square’) after copying the values to a x, y, and z vector. After I flip the y vector up down (flipud), the scatterplot looks the same. Has someone a clue why this axis is fliped in the list?
My last question is concerning the axis values. The list gives very large values for the x and y-axis while in the article of Li the values are in the range of -0.4 to 0.4. I think this is because in the article they normalize the intensity values. Is there a reason why this is not done in coloc2?
Thank you in advance for any help!