hippo_dimension_reduction {HIPPO} | R Documentation |
compute t-SNE or umap of each round of HIPPO
hippo_dimension_reduction( sce, method = c("umap", "tsne"), perplexity = 30, featurelevel = 1 )
sce |
SingleCellExperiment object with hippo object in it. |
method |
a string that determines the method for dimension reduction: either 'umap' or 'tsne |
perplexity |
numeric perplexity parameter for Rtsne function |
featurelevel |
the round of clustering that you will extract features to reduce the dimension |
a data frame of dimension reduction result for each k in 1, ..., K
data(toydata) set.seed(20200321) set.seed(20200321) toydata = hippo(toydata,K = 10,z_threshold = 1,outlier_proportion = 0.01) toydata = hippo_dimension_reduction(toydata, method="tsne") hippo_tsne_plot(toydata)