minor doc changes

fix for iss41

smart initialization bugfix when no technical covariates

prepare_results now accepts covariates in support file

PCA now made with ratios rather than counts
LeafViz now allows colour and shape of points in PCA to be set to group or covariate

Added stringr and magrittr (for leafviz)

Rebuilt C++

Change leafviz link to leafcutter.shinyapps.io/leafviz/

tools/make_cpp.R

Moved pkg to pkg

Moved pkg to pkg