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zx0223winner / HSDFinder

a tool to predict highly similar duplicates (HSDs) in eukaryotes
MIT License
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Heatmap plotting suggestion #6

Open zx0223winner opened 1 year ago

zx0223winner commented 1 year ago

Here is the enquiry email sending from a current user which might help those who have similar concerns.

I plotted the heatmap for 5 genomes. How do I make a better plot, I had 15 genomes to show. Suggestions appreciated.

zx0223winner commented 1 year ago

Hi , with regarding the heatmap you generated yesterday. Feel free to adjust the figure size which is above the Heatmap button, i,e., tuning the row number (X-axis) from 10 to 20 ~ 30, shrink the column number (Y-axis) from 45 to 50, and re-run it. Yes, right now the figure is too intense with the right hand side words. With more species you take into account(e..g, 6~8), the graph will looks better, right now there are only two species in comparison which distorted the size of the graph.

Thanks, ~Xi

zx0223winner commented 1 year ago

I tried with different column sizes, but still it looks so clumsy. I had in total ~14 genomes, How do I visualize it better?

The more species you feed into the heatmap, the shape of heatmap will look better. Try feed in 14 species into the heatmap and tune the row and column size imaging that is x-axis and y-axis of the graph. You need very large y-axis value to display the tiny words on the right. Once you have all the 14 species ready, I am happy to look at it and see if I can help you reshape the heatmap with the required data sending to me.

zx0223winner commented 1 year ago

Once you have the KO file, you can either compare different thresholds of HSDs in one species in a heatmap or HSDs from different species (if you have respective HSD result file and KO file) in a heatmap (examples attached).

Different thresholds of HSDs in one species Algae_8.pdf

HSDs from different species Danio_rerio_output_heatmap.pdf