# Looking for help - Plotting multiple graphs as once

Hello everyone,

I am currently a PhD student in Biology, and I would like some help in order to plot some graphs more efficiently than with usual built-in softwares like Numbers or Excel.
My expertise in Python programming is very weak, but I manage to understand lines of code when put in context. However, I get confused pretty quickly when alone in front of other peoples’ code.

To get into my problem :

I basically have dozens of excel-type tables, each one for every experiment, with redundant columns (experimental replica) just like this screenshot :

Every minute of the experiment up to 12h, a RFU value is measured for a specific concentration of chemicals, and I always have my “Positive Controls” somewhere in the tables.
For now, my x axis is the range of concentrations, and the y axis is the measured values (RFU).
To get my graphs, I extract an arbitrary single line (i.e a single time point) in every table to plot the results of my experiments.

Instead of extracting only one time point, I would like to gather all the data into one graph, by having a third axis (time). This could either be like a three dimensional graph, or with a ‘knob’ that would allow me to play with the third axis to see the evolution of my RFU vs Concentrations graph over time.

I’m not asking for an already made code for this task, but rather some sort of walkthrough or guide to get it done, as I suspect that it is not incredibly difficult to do so.

Thank you so much for all the help you could provide !

A popular library for data analysis in python is pandas. Pretty much any data analysis you can do in excel can also be done with pandas (filtering, pivoting, grouping, deduping, summing etc.). I’d recommend their quickstart guide as a good place to start: https://pandas.pydata.org/pandas-docs/stable/getting_started/10min.html

Pandas has an easy to use function, pd.read_excel which you can use to read an excel file using python (see https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_excel.html)

Pandas also has some plotting functionality(https://pandas.pydata.org/pandas-docs/stable/user_guide/visualization.html) which would allow you to build some line plots for a given time point.

If you want to do a 3d plot, you would need to use something like matplotlib, which is a dedicated plotting library. It would be a little more involved than using pandas built-in visualization, but would allow you to generate much more elaborate plots. Here are some examples of 3d plots made using matplotlib: https://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html. To be honest, the documentation itself might not be too beginner-friendly, but if you click the ‘source code’ link above a plot which you like the look of, it will show you the code used to generate it. Taking one of the examples and customizing it’s source code to work with your data would be a good place to start.