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navinlabcode / copykat

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Too many cells and the heatmap too big too open! #80

Open liaoshengguang opened 1 year ago

liaoshengguang commented 1 year ago

Hi,

Thanks for developing this tool! It is very cool and I am using it to call CNVs from some single-cell .

But i have some questions when i running it. 1). My data have 36601 genes, 39712 cells in raw data, and the running time is very long, i have set the cores=4. 2). Also because the 39712 cells, and the heatmap is too big about 400Mb that i can't open it. 3). At step 4, it run many iterations, but still warn NOT CONVERGENT, what can i do?

Here is my logs:

[1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "36601 genes, 39712 cells in raw data" [1] "filtered out 33 cells with less than 200 genes; remaining 39679 cells" [1] "6857 genes past LOW.DR filtering" [1] "WARNING: low data quality; assigned LOW.DR to UP.DR..." [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." [1] "step 3: smoothing data with dlm ..." [1] "step 4: measuring baselines ..." number of iterations= 217 number of iterations= 596 number of iterations= 286 number of iterations= 665 number of iterations= 316 number of iterations= 87 [1] "low confidence in classification" [1] "cell: 1" number of iterations= 374 [1] "cell: 2" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 3" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 4" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 5" number of iterations= 344 [1] "cell: 6" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 7" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 8" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 9" number of iterations= 395 [1] "cell: 10" number of iterations= 271 [1] "cell: 11" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 12" number of iterations= 344 [1] "cell: 13" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 14" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 15" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 16" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 17" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 18" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 19" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 20" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 21" number of iterations= 250 [1] "cell: 22" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 23" number of iterations= 262 [1] "cell: 24" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 25" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 26" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 27" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 28" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 29" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 30" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 31" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 32" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 33" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "step 5: segmentation..." [1] "step 6: convert to genomic bins..." [1] "step 7: adjust baseline ..." [1] "step 8: final prediction ..." [1] "step 9: saving results..." [1] "step 10: ploting heatmap ..." Time difference of 1.654129 days

Thanks so much!

Urja25 commented 1 year ago

Hi @liaoshengguang. I also generated a heatmap that is 400Mb in size and cannot open it. Did you already find a way to do so?

Thanks a lot!