About 'sinh'

[yuhuang-cst]

1. The cell-gene matrix from the same batch should be stored in the same '.csv' located in 'input_dir'. Right?
2. The values of cell-gene matrix stored in '.csv' represent the raw counts, because the 'get_data' function will transform them with 'math.asinh'. Right?
3. Why 'output_batch_correction' function doesn't take 'sinh' to get imputated raw count matrix?
   

   SAUCIE/SAUCIE.py

   Line 159 in c2e5968

   #recon = sinh(recon)

4. If '3.' holds, the data used for clustering will be transformed by 'math.asinh' twice: one is in the batch correction stage, the other is in cluster stage.

[ashipde]

It seems that for clustering, SAUCIE uses batch-corrected data (asinh values) if SAUCIE was also directed to do batch-correction. Raw data will be used if batch-correction is not specified. Thus, asinh transformation will occur only once, unless raw data are asinh values, which it seems will be so if SAUCIE is used separately to first batch-correct and then cluster (see issue #22). So having an option to output non-asinh data will be good.

(SAUCIE.py)
# CLUSTERING
if args.cluster:
    if args.batch_correct:
        input_files = sorted(glob.glob(os.path.join(args.output_dir, 'batch_corrected', '*.{}'.format(args.format))))
    else:
        input_files = rawfiles