## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE, comment = NA, fig.width = 6, fig.height = 4) library(HIPPO) library(SingleCellExperiment) ## ----eval=FALSE--------------------------------------------------------------- # devtools::install_github("tk382/HIPPO", build_vignettes = TRUE) ## ----------------------------------------------------------------------------- data(toydata) data(ensg_hgnc) ## ----eval = FALSE------------------------------------------------------------- # # X = readRDS("zhengmix4eq_counts.rds") # # toydata = SingleCellExperiment(assays = list(counts = X)) ## ----warning = FALSE---------------------------------------------------------- hippo_diagnostic_plot(toydata, show_outliers = TRUE, zvalue_thresh = 2) ## ----warning = FALSE---------------------------------------------------------- set.seed(20200321) toydata = hippo(toydata, K = 10, z_threshold = 2, outlier_proportion = 0.00001) ## ----warning = FALSE---------------------------------------------------------- toydata = hippo_dimension_reduction(toydata, method="umap") hippo_umap_plot(toydata) ## ----------------------------------------------------------------------------- toydata = hippo_dimension_reduction(toydata, method="tsne") hippo_tsne_plot(toydata) ## ----fig.width = 6, fig.height = 3-------------------------------------------- data(ensg_hgnc) zero_proportion_plot(toydata, switch_to_hgnc = TRUE, ref = ensg_hgnc) hippo_feature_heatmap(toydata, k = 3, switch_to_hgnc = TRUE, ref = ensg_hgnc, top.n = 20) ## ----------------------------------------------------------------------------- toydata = hippo_diffexp(toydata, top.n = 5, switch_to_hgnc = TRUE, ref = ensg_hgnc) ## ----------------------------------------------------------------------------- head(get_hippo_diffexp(toydata, 1)) ## ----------------------------------------------------------------------------- sessionInfo()