Step 6: Visualization - LernerLab/GuPPy GitHub Wiki

a. After the analysis is done, click on the button Open Visualization GUI

b. The Visualization GUI window will open in a new tab. In the Visualization GUI window, there are two tabs at the top left: PSTH and Heat Map

c. PSTH tab will look as shown below. In the PSTH tab, the user can visualize:

• PSTH mean trace plot
• All the PSTH traces with mean
• Combined plots for multiple events
• Any number of PSTH traces together based on user choice

To view multiple events in the bottom plot, move available events to the right using the '>>' button. To remove events from the multiple events plot, using the '<<' button.

d. Visualization GUI PSTH Options Explanation:

• Event Selector : Choose an event from the pulldown menu to display

• X and Y : X is set to timestamps, but is converted to seconds on the graphs below. Y is set to show the mean trace, but individual traces can be selected from the pulldown menu to inspect them one-by-one. The 'All' option can be selected to show all the individual traces with the mean.

• X Limit and Y Limit : The user can change the range of the x-axis & y-axis as desired using the provided sliders. Note that you can also use the box zoom and wheel zoom options available on the right of the plots. Using these options will not change the appearance of the sliders. However, if you adjust the sliders again, the plot will update based on the sliders.

• Width Plot and Height Plot : The user can customize the size of the plot using these options.

• Y Label : The plot by default simply labels the y-axis as 'y'. The user can change it here if desired.

• Save options : The user can decide to save the visualizations generated as 'png', 'svg' or in both formats using this dropdown menu. Once you are ready to save, click the 'Save' button below. You can also use the save buttons located to the right of each plot.

e. The Heat Map tab will look as shown below. In the Heat Map tab, the user can generate heatmaps showing all the events making up a PSTH in order of their occurrence, from top to bottom.

f. Visualization GUI Heatmap Options Explanation:

• Event Selector : Choose an event from the pulldown menu to display

• Color Map : Choose a color map to use for your visualization. It is important to choose a good colormap to accurately represent your data. For many applications, a perceptually uniform colormap is the best choice; i.e. a colormap in which equal steps in data are perceived as equal steps in the color space.

• By default, GuPPy selects Plasma
• We recommend using one of these four colormaps : Plasma, Magma, Inferno or Viridis
• You can do some digging about which colormap is most suitable by reading some documentation online. Here are few links which may help : http://holoviews.org/user_guide/Colormaps.html http://inversed.ru/Blog_2.htm

• Save Options : The user can decide to save the heatmap visualization as 'png', 'svg' or in both formats using this dropdown menu. Once you are ready to save, click the 'Save' button to the right.

• Width Heatmap and Height Heatmap : Use these pulldown menus to change the size of the heatmap.

f. All plots saved from the Visualization GUI will be saved into a 'saved_plots' folder within the output folder generated during earlier steps.