Man pages for Yutong441/TBdev
Infer a Trophoblast Developmental Trajectory
| add_custom_color | Customise the colors that correspond to particular features |
| add_level_to_factor | Merge factor vectors |
| add_min_max | Append minimum and maximum values |
| all_pathways_heat_pca | Draw the heatmap and PCA on genes of different pathways |
| all_vivo_all_vitro | Compare 2 DE lists between all possible combination of cells |
| append_break_labels | Append the time interval labels |
| append_if_numeric | Append string before a numeric vector |
| arrange_plots | Same function as 'grid.arrange', with the functionality of... |
| arrange_poster | Put text and figures into a poster |
| arrow_axis | Create miniature arrow to replace axes |
| arrow_to_graph | Create ggplot layers from data for plotting arrow |
| average_by_group | Average the expression matrix of Seurat by category |
| Ax3D | Draw 3D Axes |
| batch_correct | Perform Seurat batch correction |
| block_with_parameter | Run WGCNA |
| break_time_line | Obtain break points along a time line |
| cell_cycle | Genes involved in cell cycle |
| cell_heat | Plot correlation matrix |
| cell_violin | Violin plot of cell-cell similarity |
| change_expre_level | Add the mean expression level of a cell type to igraph |
| clean_metadata | Clean metadata of Seurat objects |
| colony_count | Count the number of colonies |
| colors2labels | Convert WGCNA generated names to cluster names |
| compare_cluster_enrichment | Over-representation test of genes in each cluster |
| compare_reactome | Compare reactome across multiple cell types |
| compute_all_cor | Compute the difference between every single pair of cells |
| CT | Cell type collection |
| custom_color | Customise color |
| custom_net | Customise igraph objects using ggraph |
| custom_net_diff_nets | Multiple network graphs |
| custom_net_from_seurat | Create an igraph object from seurat |
| custom_scale | Extend the axis scale |
| custom_text | Customise text appearance from 'grid.text' |
| custom_text_str | Customise text using an argument string |
| custom_tick | Make the x or y axis only show the min, middle and max points |
| cycle_over_time | Plot cycle score over pseudotime |
| data_timeline | Sample size across the timeline of the dataset |
| date_to_CS | Convert dates into Carnegie stages |
| date_to_gene | Convert date-like strings into their gene names |
| DE_gene_pairwise_list | Generate gene list for each pair of comparison |
| DE_lineage_genes | Merge DE genes and known lineage markers |
| determine_color_gradient | Obtain color gradient for heatmap |
| dim_3_to_2 | Perform coordinate transform from 3D to 2D |
| DimPlot_3D | 3D version of DimPlot |
| dim_plot_cell_similarity | Plot cell-cell similarity in a dimensionality reduction plot |
| DimPlot_labels | Obtain label positions |
| dim_red_3D | Produce 3D scatter plot using gg3D |
| dim_red_3D_traj | Add trajectory line to 3D scatterplot |
| display_cluster_enrichment | Visualise results from over-representation test |
| expand_length | Replicate a vector x to a target length target_n |
| fast_subset | Subset a Seurat object |
| filter_expression | Delete those nodes with a small expression levels |
| filter_genes | filter out genes with low expressions |
| find_DE_genes | Find DE genes across a particular feature |
| find_DE_pairwise | Find pairwise DE gene expression |
| find_eigengene | Find eigengene of WGCNA modules |
| find_peak | find the location of the maximum value |
| find_transition_from_seurat | Detect genes that show the peak changes in GP |
| format_conf | Configuration of aesthetic parameters |
| frequency_plot | Boxplot or Violin plot the count of cells expressing a... |
| gene_gene_mat | Gene expression in two categories |
| gene_name_to_entrez | Convert gene names into entrez ID |
| gene_over_pseudotime | Gene expression with uncertainty over pseudotime |
| gene_per_enriched_term | Obtain genes of each enriched terms |
| gene_per_term | For the results from 'compareClusterResult' object |
| get_all_path_view | Pathview |
| get_arrow | Obtain arrow object |
| get_cell_similarity | Calculate cell-cell similarity using quadratic programming... |
| get_DE_from_KL | Differential branching gene trajectoy analysis |
| get_gene_list | Obtain gene list from DE gene results |
| get_gene_names | Remove the 'mean_' and 'var_' prefixes from a vector |
| get_module_score | Calculate the module score of KEGG pathway |
| get_path | Obtain the path of dataset |
| get_path_genes | Obtain the gene in a particular pathway |
| get_pathway_view | Pathview |
| get_phase_score | Assign phase score |
| get_time_axis | Manually draw an x-axis |
| gg_bar | Plot barplot for overrepresented or enriched terms |
| gg_DimPlot | Reimplementation of DimPlot in Seurat for better graphic... |
| gg_plot_dim_red | Return multiple subplots |
| gg_silva | Plot forest of GSEA terms |
| GOsimp | Simplify the GO/KEGG/Reactome terms |
| graph_abs_time | Generate illustration plot for pseudotime progression |
| hub_score | Calculate intra modular connectivity |
| incorporate_TSC | Incorporate Trophoblast stem cells into Seurat object |
| integrated_seurat | Integrate expression matrix, branch information, pseudotime... |
| KeggID | KEGG ID conversion |
| Lab3D | 3D Axis Labels |
| label_transfer | Transfer the known labels from selected datasets to other... |
| lineage_markers | Lineage marker genes |
| load_all_data | load all Seurat objects specified by 'save_robj' in the... |
| load_correct_label | Load the corrected label of cells |
| make_anno_legend | Create annotation legend manually |
| make_cycle_heat | Make a heatmap for phase score |
| mat_to_seurat | Convert matrix into a list of seurat objects based on branch... |
| mean_log_likelihood | Calculate mean log likelihood |
| merge_seurat | Merge Seurat object |
| mixed_order_sort | Slight modification to 'mixedsort' |
| normalize_prob | Relative probability |
| partial_relevel | Partially relevel a vector |
| path_eigen | Draw the heatmap for the eigengene for single cell |
| pathway_heat_pca | Save the PCA and heatmap of genes in a pathway |
| pca_with_pt_line | PCA plot of cells with pseudotime trajectory projected onto... |
| peak_gene_for_heatmap | Get genes for labelling in heatmap |
| phase_density_plot | Plot the distribution of cycle phase scores as ridge/wave... |
| phase_PC_plot | Correlation of phase score with PC |
| plot_all_WGCNA_nets | Plot the gene-gene interaction network for all WGCNA clusters |
| plot_BC_filter | Investigate whether varying the size of k.filter can affect... |
| plot_cell_similarity | Plot cell-cell similarity in a line graph |
| plot_colony_count | Boxplot of the colony features in each siRNA condition |
| plot_DE_genes | Visualise DE genes |
| plot_dim_red | Quick way of plotting DimPlot in Seurat |
| plot_gene_PC | Plot the contribution of genes to each PCs |
| plot_one_branch | Plot sigmoid curve for one branch |
| plot_prob_line | Probability of fitting in river plot |
| plot_two_branch | Draw 2 sigmoid curves |
| plot_WGCNA_net | Plot gene-gene correlation network in a WGCNA cluster |
| preprocess | Preprocess the dataset generated from the quantification... |
| preprocess_df | Return parts of the dataframe 'x_df' that begins with... |
| print_dim | Print the dimension of a Seurat object |
| pseudo_real_time | Plot pseudotimee against real time |
| pseudotime_heat | Heatmap shows gene expression along the order of pseudotime... |
| p_val_all_pairs | Comparison p-value between 2 groups of DE genes |
| raw_to_seurat | Load pseudotime information to Seurat |
| remove_ribosomal_genes | Remove ribosomal genes from single cell dataset |
| rescaling | Scale data into a given range |
| return_aes_param | Obtain aesthetic settings |
| rich_forest | Barplot for GSEA results |
| ridge_all_types | Ridge plot for multiple categories |
| ridge_one_type | Ridgeplot |
| row_start_end_coord | Obtain row start and end coordinates |
| RunDiffusion | Run diffusion map |
| run_dim_red | Run DR |
| RunGPLVM | Add GPLVM data to Seurat dim red assay |
| run_GSEA | GSEA |
| run_GSEA_all_types | Combine the GSEA results from all clusters |
| run_GSEA_pairwise | Run pairwise GSEA |
| sagittae | Draw the arrow sign for 'rich_forest' |
| save_DE_genes | Save Differentially Expressed Genes |
| save_DE_pairwise | Save pairwise DE gene in excel files |
| save_for_10X | Store 10X data |
| save_hub_score | Save the hub score data frame |
| save_indiv_plots | Save a list of plots individually |
| save_peak_genes | Save peak genes in a particular KEGG pathway |
| save_to_csv | Save Seurat object as csv |
| scaling | Perform row or column scaling |
| Seg3D | Extention to 'Ax3D' with arrow heads |
| selected_cell_PCA | Run PCA on selected population of cells |
| seurat_heat | Heatmap for Seurat object |
| seurat_heat_highlight | Highlight parts of a heatmap |
| seurat_heat_split | Splitting heatmap by feature |
| seurat_list_score | Calculate the pathway module score for the Seurat object for... |
| seurat_violin | Similar to Seurat VlnPlot, with more graphic controls |
| seurat_volcano | Deseq2 style Volcano plot |
| sigmoid | Use sigmoid function to draw the curve |
| signif_p_val | Filter significant pairs of DE genes |
| sim_emap | Plot enrichment pie chart with simplified terms |
| sparsify | Sparsify a large matrix |
| standardise_name | Standardise cell labels |
| Stat3D | Draw 3D Geoms |
| strong_gene_violin | violin plot on genes that contribute to latent dimensions |
| subset_celltype | Select Seurat object by cell type |
| subset_terms | Show terms from specific groups |
| summarise_gsea | Summarise the raw GSEA dataframe |
| term_gene_labels | Obtain the label information for enrichment barplot |
| text_3D_repel | 3D version of 'geom_text_repel' |
| TF | A list of transcriptional factors |
| TF_enrichment_pairwise | Compare TF motif enrichment between cell types |
| theme_dim_red | Theme for DimPlot |
| theme_TB | Append this function at the end of a ggplot to provide the... |
| time_cluster_plot | Plot the clustering results of times against the peak... |
| unique_DE_genes | Select the top DE genes from each cluster |
| wrap_long_sentence | Line break after very long words |
| write_module_gene | Record genes of a particular module |
