Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data

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Documentation for package ‘fastTopics’ version 0.6-186

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

compare_fits	Summarize and Compare Model Fits
cost	NMF and Topic Model Likelihoods and Deviances
deviance_poisson_nmf	NMF and Topic Model Likelihoods and Deviances
de_analysis	Differential Expression Analysis using a Topic Model
de_analysis_control_default	Differential Expression Analysis using a Topic Model
embedding_plot_2d	PCA, t-SNE and UMAP Plots
embedding_plot_2d_ggplot_call	PCA, t-SNE and UMAP Plots
fit_multinom_model	Fit Simple Multinomial Model
fit_poisson_nmf	Fit Non-negative Matrix Factorization to Count Data
fit_poisson_nmf_control_default	Fit Non-negative Matrix Factorization to Count Data
fit_topic_model	Simple Interface for Fitting a Multinomial Topic Model
init_poisson_nmf	Fit Non-negative Matrix Factorization to Count Data
init_poisson_nmf_from_clustering	Fit Non-negative Matrix Factorization to Count Data
loadings_plot	Loadings Plot
loadings_plot_ggplot_call	Loadings Plot
loglik_multinom_topic_model	NMF and Topic Model Likelihoods and Deviances
loglik_poisson_nmf	NMF and Topic Model Likelihoods and Deviances
loglik_vs_rank_ggplot_call	Plot Log-Likelihood Versus Rank
merge_topics	Combine Topics in Multinomial Topic Model
multinom2poisson	Recover Poisson NMF Fit from Multinomial Topic Model Fit
pbmc_facs	Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq data
pca_from_topics	Low-dimensional Embeddings from Poisson NMF or Multinomial Topic Model
pca_hexbin_plot	PCA, t-SNE and UMAP Plots
pca_hexbin_plot_ggplot_call	PCA, t-SNE and UMAP Plots
pca_plot	PCA, t-SNE and UMAP Plots
plot.multinom_topic_model_fit	Structure Plot
plot.poisson_nmf_fit	Structure Plot
plot.topic_model_de_analysis	Volcano Plots for Visualizing Results of Differential Expression Analysis
plot_loglik_vs_rank	Plot Log-Likelihood Versus Rank
plot_progress	Plot Progress of Model Fitting Over Time
poisson2multinom	Recover Multinomial Topic Model Fit from Poisson NMF fit
predict.multinom_topic_model_fit	Predict Methods for Poisson NMF and Multinomial Topic Model
predict.poisson_nmf_fit	Predict Methods for Poisson NMF and Multinomial Topic Model
print.summary.multinom_topic_model_fit	Summarize Poisson NMF or Multinomial Topic Model Fit
print.summary.poisson_nmf_fit	Summarize Poisson NMF or Multinomial Topic Model Fit
run_homer	Perform HOMER Motif Enrichment Analysis using DE Genomic Positions
select	Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit
select.multinom_topic_model_fit	Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit
select.poisson_nmf_fit	Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit
select_loadings	Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit
simulate_count_data	Simulate Count Data from Poisson NMF Model
simulate_multinom_gene_data	Simulate Gene Expression Data from Poisson NMF or Multinomial Topic Model
simulate_poisson_gene_data	Simulate Gene Expression Data from Poisson NMF or Multinomial Topic Model
simulate_toy_gene_data	Simulate Toy Gene Expression Data
structure_plot	Structure Plot
structure_plot_default_embed_method	Structure Plot
structure_plot_ggplot_call	Structure Plot
summary.multinom_topic_model_fit	Summarize Poisson NMF or Multinomial Topic Model Fit
summary.poisson_nmf_fit	Summarize Poisson NMF or Multinomial Topic Model Fit
tsne_from_topics	Low-dimensional Embeddings from Poisson NMF or Multinomial Topic Model
tsne_plot	PCA, t-SNE and UMAP Plots
umap_from_topics	Low-dimensional Embeddings from Poisson NMF or Multinomial Topic Model
umap_plot	PCA, t-SNE and UMAP Plots
volcano_plot	Volcano Plots for Visualizing Results of Differential Expression Analysis
volcano_plotly	Volcano Plots for Visualizing Results of Differential Expression Analysis
volcano_plot_do_label_default	Volcano Plots for Visualizing Results of Differential Expression Analysis
volcano_plot_ggplot_call	Volcano Plots for Visualizing Results of Differential Expression Analysis
volcano_plot_ly_call	Volcano Plots for Visualizing Results of Differential Expression Analysis