Man pages for wmacnair/psupertime
Psupertime is supervised pseudotime for single cell RNAseq data
| dot-calc_clusters_dt | make nice data.table of hierarchical clusters |
| dot-calc_expressed_genes | Restrict to genes with minimum proportion of expression... |
| dot-calc_hvg_genes | Calculates list of highly variable genes (according to... |
| dot-check_conf_params | Check variables for confusion matrices |
| dot-check_params | check all parameters |
| dot-check_x | Checks the gene info |
| dot-check_y | Checks the labels |
| dot-do_topgo_for_cluster | Calculate GO enrichment for each cluster vs all other genes |
| dot-get_test_idx | Get list of cells to keep aside as test set |
| dot-get_tf_list | Get list of transcription factors |
| dot-glmnetcr_propn | This is based on an equivalent function from the package... |
| dot-make_best_beta | Extracts best coefficients. |
| dot-make_col_vals | Define RColorBrewer palette to use; default is RdBu. |
| dot-make_plot_dt | Internal function |
| dot-make_x_data | Process input data |
| dot-psummarize | Text to summarize psupertime object |
| dot-restrict_to_y_labels | Use y_labels to define cells to use, and order of labels |
| dot-select_genes | Select genes for use in regression |
| double_psupertime | Projects two different psupertimes onto each other |
| plot_double_psupertime | Projects two different psupertimes onto each other, using... |
| plot_double_psupertime_confusion | Plots the confusion matrices of two psupertime objects... |
| plot_double_psupertime_contour | Projects two different psupertimes on top of each other |
| plot_double_psupertime_genes | Compares coefficients for genes learned from different... |
| plot_go_results | Plots the significant GO terms for each cluster |
| plot_heatmap_of_gene_clusters | Plot heatmap of gene clusters |
| plot_identified_gene_coefficients | Plots top coefficients |
| plot_identified_genes_over_psupertime | Plots profiles of identified genes against psupertime. |
| plot_labels_over_psupertime | Plots labels over their projected values on psupertime. |
| plot_new_data_over_psupertime | Plots profiles of hand-selected genes against psupertime. |
| plot_predictions_against_classes | Plots confusion matrix of true labels against predicted... |
| plot_profiles_of_gene_clusters | Plot heatmap of gene clusters |
| plot_specified_genes_over_psupertime | Plots profiles of hand-selected genes against psupertime. |
| plot_train_results | Plot results of training |
| project_onto_psupertime | Gives projection of data onto psupertime (either using... |
| psupertime | Supervised pseudotime |
| psupertime_go_analysis | GO enrichment analysis for genes learned from different... |
| psupertime_go_analysis_old | GO enrichment analysis for genes learned from different... |
| psupertime_plot_all | Convenience function to do multiple plots |
| tf_human | List of human transcription factors |
| tf_mouse | List of mouse transcription factors |
