Tutorial update

[JEFworks]

From Nikolas:

"The last lines of the tutorial with the tSNE embedding don't quite work out of the box. You may want to substitute with the following:

tSNE.pagoda <- Rtsne(cell.clustering$distance,is_distance=T,initial_dims=100,perplexity=10)

embed.tSNE <- tSNE.pagoda$Y

rownames(embed.tSNE) <- cell.clustering$clustering$labels

app <- make.pagoda.app(tamr2, tam, varinfo, go.env, pwpca, clpca, col.cols = col.cols, cell.clustering = hc, title = "NPCs", embedding = embed.tSNE)"