Log output
I think the log output can be improved. Here an example along with my suggestions, which can be applied for other output also:
...
INFO [2022-08-01 17:26:14] Differential expression will be filltered by 0.2 pvalue and 1 logFC
...
INFO [2022-08-01 17:47:43] Preparing the Gene-TF Matrix
INFO [2022-08-01 17:47:44] The matrix has been created
INFO [2022-08-01 17:47:44] Finished sucessfully. Execution time: 1.2 secs
INFO [2022-08-01 17:47:44] Final data prepration finished
INFO [2022-08-01 17:47:44] The dimensions of final matrix are ( 959 , 271 )
INFO [2022-08-01 17:47:44] Finished sucessfully. Execution time: 0 secs
INFO [2022-08-01 17:48:41] Maching learning model Finished
INFO [2022-08-01 17:48:41] Finished sucessfully. Execution time: 56.8 secs
...
INFO [2022-08-01 18:06:23] Actual network number : 9
INFO [2022-08-01 18:08:45] Maching learning model Finished
INFO [2022-08-01 18:08:45] Finished sucessfully. Execution time: 2.4 mins
...
INFO [2022-08-01 17:48:41] Complete Random dataset successfully finished
INFO [2022-08-01 17:48:41] Finished sucessfully. Execution time: 4.7 mins
INFO [2022-08-01 17:48:41] Finished sucessfully. Execution time: 22.4 mins
[1] "finished!"
- first line: improve phrasing, clarify what "1 logFC" means here (i.e., the absolute value if I am correct), and give dataset dimensions before and after the filtering
- the last line is missing the flog.info I think
- the last 2 flog.info messages have the same intendation, once 4.7 minutes, once 22.4, what are they for?
- is the dimensionality before any filtering also given? It should be so it can be more easily seen what is being filtered out
- a task that needs one second ( Preparing the Gene-TF Matrix ) doesnt need two separate lines, keep the output as short as possible and as long as necessary. Execution time for tasks that generally take only a few seconds are not needed IMHO.
- the indentation can be improved and help to associate output lines to where they belong. For example, the line "Maching learning model Finished" should have a space more because it belongs to the "Actual network number" block.
Edited by Christian Arnold