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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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Adding delta PCC to AMALGKIT output #152

Open Hego-CCTB opened 1 month ago

Hego-CCTB commented 1 month ago

I added delta PCC to the AMALGKIT output as shown on the paper figure, like this: uncorrected Malus_domestica.2.correlation_cutoff.pdf corrected Malus_domestica.2.correlation_cutoff.sva.pdf

I also added a table to the output, which contains mean PCC, median PCC and variance for each boxplot category (bwbw, bwwi, wiwi, wibw) and each round. This is the data I used for the cross-species delta PCC plots of the paper figure. Here's how the table looks like: Malus_domestica.sva.correlation_statistics.zip

Should I add these plots to csca output?

If it is OK like this, I'll push the update!

kfuku52 commented 1 month ago

The plot looks good, and the table would be useful. Please proceed with pushing the update. I also look forward to the csca update as well.

Hego-CCTB commented 3 weeks ago

https://github.com/kfuku52/amalgkit/commit/36428a5f2245e41cbb92ad2402d4e83c1e52ece5

I added the PCC plots to csca as well! This is how they look like: csca_delta_pcc_boxplot.pdf

The style is a bit different from the figure I made for the paper since those plots were done in Python, but now the styles are consistent between the PCC and delta PCC plots.

kfuku52 commented 3 weeks ago

Thank you! If "Group" refers to the sample_group column, using "Sample group" will make its meaning clearer. Some of the curate plots may still display legacy labels like "Organ", but they should now be updated to "Sample group" as well. Could you please make these corrections?

Hego-CCTB commented 3 weeks ago

Good points! I'll update the PCC plots and legacy labels!