Do not modify df in place

added 4 commits

• f7848bd3 - apply threshold in correlation matrix
• 0c38dbe7 - modify help
• 3e2647d0 - fix missing option in cli
• bbd58276 - Minor fix on cache_only option and fix on conflicts on plotting options

Compare with previous version

enabled an automatic merge when the pipeline for bbd58276 succeeds

merged

mentioned in commit 33ac8589