Changed some plot.graphics and plot.matrices to plotGraphics and plotMatrices

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Changed the vignette format from Sweave to knitr

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>