Interpreting the output image about pieparty

[harbourlab]

I will get back to you this weekend!

[harbourlab]

Could you please provide the exact command you use to execute PieParty?

[thugib]

This is the command: matthew@OptiPlex-7071:~/python/PieParty-master$ python3 PieParty.py -g /home/matthew/python/ABCpm_anchored_dcX30_resp5_geneexp.csv -c /home/matthew/python/ABCpm_anchored_dcX30_resp5_cellcoord.csv -l /home/matthew/python/QC5.csv And this is the output: PieParty Version 1.3 starting Done calculating! Baking the pies now. /home/matthew/.local/lib/python3.6/site-packages/PIL/Image.py:2835: DecompressionBombWarning: Image size (169000000 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.   DecompressionBombWarning, 1882 cells plotted Matthew

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On 9/11/20 10:17 PM, Harbour Ocular Oncology Laboratory wrote:         External Email - Use Caution Could you please provide the exact command you use to execute PieParty? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB53TZOA3HUK5GMVLQ6ZULSFLK4HANCNFSM4RISR4DQ>.

[harbourlab]

Thanks! I'm working on it. I'll have a new version uploaded tomorrow which will plot a legend, so that you know which gene is what. The pink is indeed a bug, which i need to fix. There should not be a pink - seems to be a thing when small gene lists are plotted. (Edit: The pink color is actually correct, see below)

[thugib]

OK. Thank you very much for your help. I was thinking that maybe I could just put one gene in a list and do multiple lists and specify a color for each list. Matthew

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On 9/13/20 10:02 PM, Harbour Ocular Oncology Laboratory wrote:         External Email - Use Caution Thanks! I'm working on it. I'll have a new version uploaded tomorrow which will plot a legend, so that you know which gene is what. The pink is indeed a bug, which i need to fix. There should not be a pink. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB53T5OC2RRJ4TRO26H6ETSFV2S3ANCNFSM4RISR4DQ>.

[harbourlab]

Alright, I did some checking and the pink is actually correct. The dark blue the "viridis" color scale starts with is actually a dark pink, which turns really pink when brightened. I will upload a new version of PieParty in a minute (version 1.5), which will now generate a "labels.svg" output file, explaining the output.

Your input was very valuable, and I'm still working on adding some more features to PieParty. Please let me know if you have any more questions or run into problems. Also if you are missing a feature that would be helpful for your work please let me know!

[thugib]

Thank you very much for your help. I thought of one thing that may be helpful. I always get the following warning when I run PieParty.py: /home/matthew/.local/lib/python3.6/site-packages/PIL/Image.py:2835: DecompressionBombWarning: Image size (169000000 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.   DecompressionBombWarning,     I thought it may be helpful to warn people that this message may come up and to ignore it if it does. The message may scare some people away from using PieParty. Matthew

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On 9/14/20 2:32 PM, Harbour Ocular Oncology Laboratory wrote:         External Email - Use Caution Alright, I did some checking and the pink is actually correct. The dark blue the "viridis" color scale starts with is actually a dark pink, which turns really pink when brightened. I will upload a new version of PieParty in a minute (version 1.4), which will now generate a "labels.svg" output file, explaining the output. Your input was very valuable, and I'm still working on adding some more features to PieParty. Please let me know if you have any more questions or run into problems. Also if you are missing a feature that would be helpful for your work please let me know! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB53T3G3GYX45BE4CKRKCDSFZOVPANCNFSM4RISR4DQ>.

[harbourlab]

Very true! The new version will output an explainer.. I will put one on the github site too. Thanks!! Let me know if everything works for you!