Too many cells and the heatmap too big too open!

Start by reproducing the copykat v1.1.0 run described in the issue with 36,601 genes and 39,712 cells using cores=4. Inspect step 4's repeated NOT CONVERGENT warnings and step 10's 400 MB heatmap output; done should include an explanation or reproducible fix for the runtime, convergence, and heatmap-size problems.

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!