Issues in moving decontX functions from celda to decontX

[yuan-yin-truly]

• 4 functions from celda/R/celda_function.R moved to decontX/R/celda_function.R. Of the 4, normalizeCounts() and retrieveFeatureIndex() has roxygen example that requires dataset celdaCGSim. If celdaCGSim is not required anywhere else in decontX, consider update example and remove the dataset from package. Otherwise if normalizeCounts() and retrieveFeatureIndex() are needed for celda package, consider removing them in decontX/R/celda_function.R and use celda::normalizeCounts(), celda::retrieveFeatureIndex().
• Dimension reduction plots (such as plotDimReduceCluster() and plotDimReduceFeature()) are not added to decontX. If they are not used in celda, consider moving them to decontX. Otherwise, call celda::plotDimReduceCluster() when needed.

[yuan-yin-truly]

Work on branch decontX_func

[yuan-yin-truly]

For point 1, normalizeCounts() is used by celda. Removed it from decontX repo and called celda::normalizeCounts() when needed. retrieveFeatureIndex() is only used by decontX related functions. Kept in decontX repo and rewrote its Roxygen example. Removed celdaCGSim dataset from decontX repo.

[yuan-yin-truly]

For point 2, call celda:: when needing dimension reduction plots for now.