Giotto: Cleanup some dependencies

[jiajic]

Move to Suggests:

• [x] Rtsne
• [x] plotly
• [x] ggrepel
• [x] limma

Isolate to GiottoVisuals

• [x] cowplot

Move to GiottoUtils

• [x] jsonlite
• [x] progressr
• [x] reshape2

[jiajic]

GiottoUtils changes to be implemented in version 0.1.12

• jsonlite:
  • read_json() and fromJSON() are both re-exported since both are used in Giotto. In the future, we can move towards only using one of these and remove the other from GiottoUtils.
• progressr:
  • progressor() and with_progress() are now re-exported from GiottoUtils as pbar() and with_pbar(), respectively.
• reshape2:
  • We do not actually use functions in reshape2 outside of dcast() for matrix and data.frame. The data.table::dcast() supercedes the data.frame method. For the matrix method, we now implement melt_matrix() which produces identical results (with the use cases in Giotto at least).

[jiajic]

GiottoVisuals changes to be implemented in version 0.2.5

• cowplot:
  • reexport of plot_grid()