Added the functionality of scale.factor in NormalizeData being set to "median" of counts #9389
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Background
The NormalizeData generic has several different implementations depending on the class of the first object passed as a parameter to the method. These are NormalizeData.Assay, NormalizeData.default, NormalizeData.Seurat, NormalizeData.StdAssay, and NormalizeData.V3Matrix*. Each of these methods has three possible in-built normalization methods: "LogNormalize", "CLR" and "RC". Excluding "CLR", the other two methods make use of a scale.factor parameter to multiply the normalized values during the normalization process. This value is defaulted to 1e4 for LogNormalize and 1 for RelativeCounts (RC).
Updates
I have added in the capacity for the implementations of LogNormalize, RelativeCounts and .SparseNormalize to compute the median of the counts across all columns (cells) (or rows (genes) if margin = 1L in the case of LogNormalize.default) and use this as the scale.factor, if the value passed to the scale.factor parameter is "median".
I have also tested the modifications to these functions by writing unit tests in test_preprocessing.R that make sure that the median is being computed correctly if the value passed to the scale.factor parameter is "median".