To repeat the real data analyses for the MEF reprogramming time course:
- Download the FCS files from Cytobank for accession number 43324, and put them in
refdata/Cytobank_43324
. - Enter
refdata
and runpreprocess_43324.R
to transform and gate on the intensities, followed bygen_objects_43324.R
to obtain the hypersphere counts. - Enter
real/analysis
and run (in order)detect_da.R
, to detect DA hyperspheres;plot_da_initial.R
, to construct the t-SNE plots;plot_da_extra.R
, to construct subpopulation- and time-point-specific plots; andplot_dispersions.R
, to construct the dispersion plot. Note that the t-SNE plots are stochastic and may not be the same as in the paper.
Alternatively, you can look at workflow.Rmd
in real/workflow
, which provides an annotated workflow of the processing and analysis of the Oct4-GFP time course data.
To run the additional analyses for the time course data:
- Enter
real/neighbours
and runget_neighbors.R
to construct plots of distances to nearest neighbours. - Enter
real/robustness
and runrobustness.R
to obtain DA statistics with different parameter settings. - Enter
real/clustering
and runcitrus_test.R
to obtain DA clusters from CITRUS. Then runmap_onto_tsne_citrus.R
to map the CITRUS cluster centres onto the t-SNE plot from the hypersphere analysis.
To run the analyses for the BMMC data:
- Download the FCS files from Cytobank for accession number 44185, and put them in
refdata/Cytobank_44185
. - Enter
refdata
and runpreprocess_44185.R
to transform and gate on the intensities, followed bygen_objects_44185.R
to obtain the hypersphere counts. - Enter
real/secondary
and run (in order)detect_da.R
, to detect DA hyperspheres; andplot_da.R
, to construct the t-SNE plots.
To repeat the simulations, enter simulations
and run:
edgeR_check.R
, to check type I error control.FDR_check.R
, to check spatial FDR control.cluster_sim.R
, to check performance of clustering.radius_sim.R
, to check the effect of increasing the radius on hypersphere positions.shift_check.R
, to check the type I error control on intensity-shifted data.