Fixing reproducibility/seed issues with multiple functions

[irzamsarfraz]

• .withSeed internal function does not seem to fix the seed and computes random results every time (for now using withr::with_seed directly) in many functions including scaterPCA and scaterUMAP
• Added seed to runHarmony function
• Added seed to runSeuratFindClusters function

[codecov]

Codecov Report

Attention: 117 lines in your changes are missing coverage. Please review.

Comparison is base (5e9e1a6) 52.76% compared to head (2f9d9db) 52.72%.
Report is 12 commits behind head on devel.

❗ Current head 2f9d9db differs from pull request most recent head 116a9fe. Consider uploading reports for the commit 116a9fe to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #723      +/-   ##
==========================================
- Coverage   52.76%   52.72%   -0.05%     
==========================================
  Files          79       79              
  Lines       12695    12703       +8     
==========================================
- Hits         6699     6698       -1     
- Misses       5996     6005       +9     

Files	Coverage Δ
R/doubletFinder_doubletDetection.R	76.68% <100.00%> (ø)
R/miscFunctions.R	47.29% <ø> (-1.98%)	⬇️
R/runCluster.R	80.58% <100.00%> (ø)
R/runTSNE.R	78.26% <100.00%> (ø)
R/runUMAP.R	81.53% <100.00%> (ø)
R/scDblFinder_doubletDetection.R	80.95% <100.00%> (ø)
R/scater_PCA.R	100.00% <100.00%> (ø)
R/scds_doubletdetection.R	84.93% <100.00%> (ø)
R/seuratFunctions.R	73.30% <100.00%> (+0.09%)	⬆️
R/runBatchCorrection.R	21.48% <0.00%> (-0.08%)	⬇️
... and 1 more

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