# Generated by roxygen2: do not edit by hand

S3method(plot,multinom_topic_model_fit)
S3method(plot,poisson_nmf_fit)
S3method(plot,topic_model_de_analysis)
S3method(predict,multinom_topic_model_fit)
S3method(predict,poisson_nmf_fit)
S3method(print,summary.multinom_topic_model_fit)
S3method(print,summary.poisson_nmf_fit)
S3method(select,multinom_topic_model_fit)
S3method(select,poisson_nmf_fit)
S3method(summary,multinom_topic_model_fit)
S3method(summary,poisson_nmf_fit)
export(annotation_heatmap)
export(compare_fits)
export(cost)
export(de_analysis)
export(de_analysis_control_default)
export(deviance_poisson_nmf)
export(embedding_plot_2d)
export(embedding_plot_2d_ggplot_call)
export(fit_multinom_model)
export(fit_poisson_nmf)
export(fit_poisson_nmf_control_default)
export(fit_topic_model)
export(init_poisson_nmf)
export(init_poisson_nmf_from_clustering)
export(loadings_plot)
export(loadings_plot_ggplot_call)
export(loglik_multinom_topic_model)
export(loglik_poisson_nmf)
export(loglik_vs_rank_ggplot_call)
export(merge_topics)
export(multinom2poisson)
export(pca_from_topics)
export(pca_hexbin_plot)
export(pca_hexbin_plot_ggplot_call)
export(pca_plot)
export(plot_loglik_vs_rank)
export(plot_progress)
export(poisson2multinom)
export(run_homer)
export(select_loadings)
export(simulate_count_data)
export(simulate_multinom_gene_data)
export(simulate_poisson_gene_data)
export(simulate_toy_gene_data)
export(structure_plot)
export(structure_plot_default_embed_method)
export(structure_plot_ggplot_call)
export(tsne_from_topics)
export(tsne_plot)
export(umap_from_topics)
export(umap_plot)
export(volcano_plot)
export(volcano_plot_do_label_default)
export(volcano_plot_ggplot_call)
export(volcano_plot_ly_call)
export(volcano_plotly)
import(Matrix)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Rcpp,evalCpp)
importFrom(RcppParallel,RcppParallelLibs)
importFrom(RcppParallel,defaultNumThreads)
importFrom(RcppParallel,setThreadOptions)
importFrom(RhpcBLASctl,blas_get_num_procs)
importFrom(RhpcBLASctl,blas_set_num_threads)
importFrom(Rtsne,Rtsne)
importFrom(ashr,ash)
importFrom(cowplot,plot_grid)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,select)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_q)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_bin_hex)
importFrom(ggplot2,theme)
importFrom(ggplot2,waiver)
importFrom(ggrepel,geom_text_repel)
importFrom(graphics,plot)
importFrom(gtools,rdirichlet)
importFrom(htmlwidgets,saveWidget)
importFrom(irlba,irlba)
importFrom(methods,as)
importFrom(parallel,splitIndices)
importFrom(pbapply,pblapply)
importFrom(pbapply,pboptions)
importFrom(plotly,hide_colorbar)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(progress,progress_bar)
importFrom(quadprog,solve.QP)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(stats,dpois)
importFrom(stats,formula)
importFrom(stats,glm)
importFrom(stats,glm.control)
importFrom(stats,kmeans)
importFrom(stats,pnorm)
importFrom(stats,poisson)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,rmultinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(stats,summary.glm)
importFrom(utils,combn)
importFrom(utils,modifyList)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(uwot,umap)
useDynLib(fastTopics)
