Original TOBIAS Manuscript Figure 2--Nature Communications volume 11, Article number: 4267 (2020)

[c2b2pss]

Hi,

How was the impressive Figure 2 in your original TOBIAS manuscript generated? It is a very clear way to examine progression of binding sites etc..

1. Was this all done through TOBIAS?
2. For Figure 2b, the left panel heatmap showing TF vs stage clustering -- Is that doable in TOBIAS?
3. If step (2) above is from TOBIAS, I guess one then chooses which footprint to generate?
4. Is it possible to provide sample code for the heat map and the footprints?
5. **Even if you used heatmap functionalities outside TOBIAS, I would immensely appreciate tsample code. If you feel it better to email me please feel free to do so. (ps2536 at cumc dot columbia dot edu)

I have 3 conditions (with replicates each) over a long treatment period, and would like to look at the progression across these. Your figure is extremely concise and informative.

Thanks!

[mohobein]

Hey @c2b2pss,

thank you for your issue. For the most part, the figure was custom-made for the publication and was not directly generated using TOBIAS functions.

For Figure 2a and 2c, there is an R script using the package ComplexHeatmap to generate them, but since it it very specific to the dataset and the analysis in the paper, it would have to be reworked and cleaned up to be easily applicable to general use cases. It is probably easier if you build it from scratch for your purposes. A good example on how to do that can be found here.

Figure 2b can be generated using the command TOBIAS PlotAggregate (apart from some stylistic adjustments that were done for the publication). Usage instructions can be found in the wiki. To replicate the figure, you'd need to provide the binding sites of each TF of interest separately via --TFBS and the corrected signal tracks for each of your time points via --signals.

I hope this helps you to visualize changes across your treatment period! If you have further questions, feel free to ask.

Best regards, the TOBIAS team