Man pages for TransProR
Analysis and Visualization of Multi-Omics Data
| add_boxplot | Add a boxplot layer to a 'ggtree' plot |
| add_new_tile_layer | Add a new tile layer with dynamic scales to a 'ggtree' plot |
| adjust_alpha_scale | Adjust Alpha Scale for Data Visualization |
| adjust_color_tone | Adjust Color Tone by Modifying Saturation and Luminance |
| adjust_export_pathway | Adjust and Export Pathway Analysis Results |
| all_degs_venn | All DEGs Venn Diagram Data |
| circos_fruits | Add multiple layers to a 'ggtree' plot for visualizing gene... |
| Combat_Normal | Process and Correct Batch Effects in TCGA's normal tissue and... |
| combat_tumor | Process and Correct Batch Effects in Tumor Data |
| compare_merge | Compare and merge specific columns from two DEG data frames |
| Contrast_Venn | Function to Create a Venn Diagram of DEGs with Custom Colors |
| create_base_plot | Create a base plot with gene expression data on a... |
| deg_filter | Function to Filter Differentially Expressed Genes (DEGs) |
| DESeq2_analyze | Differential Gene Expression Analysis using 'DESeq2' |
| drawLegends | Draw Dual-Sided Legends on a Plot |
| edgeR_analyze | Differential Gene Expression Analysis using 'edgeR' |
| enrich_circo_bar | Combine and Visualize Data with Circular Bar Chart |
| enrichment_circlize | Draw Chord Diagram with Legends |
| enrichment_spiral_plots | Create Spiral Plots with Legends Using 'spiralize' and... |
| enrich_polar_bubble | Enrichment Polar Bubble Plot |
| extract_descriptions_counts | Extract and Count Descriptions with Specified Color |
| extract_ntop_pathways | Extract and Store Top Pathways for Each Sample |
| extract_positive_pathways | Extract Positive Pathways from SSGSEA Results and Select... |
| facet_density_foldchange | Create faceted high-density region plots with optional points... |
| filter_diff_genes | Filter Differentially Expressed Genes |
| four_degs_venn | Function to Create a Venn Diagram of DEGs |
| gather_graph_edge | Gather graph edge from data frame Please note that this... |
| gather_graph_node | Gather graph nodes from a data frame Please note that this... |
| gene_color | Merge Genes with Color Information Based on Up/Down... |
| gene_highlights | Add gene highlights to a ggtree object |
| gene_map_pathway | Create Pathway-Gene Mapping Data Frame |
| get_gtex_exp | Get GTEx Expression Data for Specific Organ |
| get_tcga_exp | TCGA Expression Data Processing |
| gtree | Phylogenetic Tree Object |
| highlight_by_node | Highlight Nodes in a Phylogenetic Tree with Custom Fill... |
| highlight_genes | Add Highlights for Genes on a Phylogenetic Tree |
| limma_analyze | Differential Gene Expression Analysis using limma and voom |
| log_transform | Log transformation decision and application on data |
| merge_density_foldchange | Create high-density region plot with optional points, density... |
| merge_gtex_tcga | Merge gene expression data from GTEx and TCGA datasets |
| merge_id_position | Merge Data Frames by Common Row Names with Additional Columns |
| merge_method_color | Merge Data Frames with Specific Method and Color Columns |
| new_ggraph | Generate a graphical representation of pathway gene maps |
| pathway_count | Count Genes Present in Pathways Above a Threshold |
| pathway_description | Describe Genes Present in Selected Pathways |
| pipe | Pipe operator |
| prep_deseq2 | Prepare DESeq2 data for plotting |
| prep_edgeR | Prepare edgeR DEG data for plotting |
| prep_limma | Prepare limma-voom DEG data for plotting |
| prep_wilcoxon | Prepare Wilcoxon DEG data for plotting |
| process_heatdata | Process Heatmap Data with Various Selection Options |
| seek_gtex_organ | Load and Process GTEX Phenotype Data to Retrieve Primary Site... |
| selectPathways | Randomly Select Pathways with Limited Word Count |
| spiral_newrle | Render a Spiral Plot Using Run-Length Encoding |
| Wilcoxon_analyze | Differential Gene Expression Analysis Using Wilcoxon Rank-Sum... |
