Fix pVACview warnings related to deprecated methods

[malachig]

When running pVACview locally I observe several warnings with the latest version of R that I hope would be relatively easy to fix:

reshape2 is superseded

Warning in dcast(peptide_columns_mt, Mutant ~ hla_types, value.var = "ic50s_MT") :
  The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(peptide_columns_mt). In the next version, this warning will become an error.

fun.y, fun.ymin. and fun.ymax are deprecated

Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
ℹ Please use the `fun` argument instead.
Warning: The `fun.ymin` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
ℹ Please use the `fun.min` argument instead.
Warning: The `fun.ymax` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
ℹ Please use the `fun.max` argument instead.

sizes parameter is unknown in geom_jitter

Warning in geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms),  :
  Ignoring unknown parameters: `sizes`

**size argument of element_line is deprecated

Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.