Add marker visualizations

asmagen / robustSingleCell

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

http://dx.doi.org/10.1016/j.celrep.2019.10.131

MIT License

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Add marker visualizations #3

Closed asmagen closed 5 years ago

asmagen commented 5 years ago

Added tSNE overlay and flow-like plots. @Mamie We may want to add an example of using these functions to the tutorial (using the same downsampled dataset you used there). E.g.: plot.contour.overlay.tSNE (LCMV1,genes = 'Cd8a') plot.pair.scatter (LCMV1,gene1 = 'Cxcr5',gene2 = 'Tcf7',cluster_group1 = c('Tfh','Tcmp'),cluster_group2 = c('CD8','Cycle_CD8'),group1_label = 'Tfh_Tcmp',group2_label = 'CD8')

Mamie commented 5 years ago

[x] Add usage of plot.contour.overlay.tSNE and plot.pair.scatter to vignette and README.Rmd
[x] fix test-clustering.R to initialize work path in TMPDIR instead of modifying users' home filespace