# Analysis and Visualization of Multi-Omics Data

## Documentation for package ‘TransProR’ version 0.0.6

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

## Help Pages

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 expression and enrichment data
Combat_Normal | Process and Correct Batch Effects in TCGA's normal tissue and GTEX Data
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 phylogenetic tree
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'
enrichment_circlize | Draw Chord Diagram with Legends
enrichment_spiral_plots | Create Spiral Plots with Legends Using 'spiralize' and 'ComplexHeatmap'
enrich_circo_bar | Combine and Visualize Data with Circular Bar Chart
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 Random Samples
facet_density_foldchange | Create faceted high-density region plots with optional points and density contours
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 function is from the 'ggraph' package and has not been altered in functionality, but it has been optimized and iterated. It is not original content of 'TransProR'. However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR', the author directly referenced the involved functions in 'TransProR'. This is not the author's original creation. All users please be aware!

gather_graph_node

Gather graph nodes from a data frame Please note that this function is from the 'ggraph' package and has not been altered in functionality, but it has been optimized and iterated. It is not original content of 'TransProR'. However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR', the author directly referenced the involved functions in 'TransProR'. This is not the author's original creation. All users please be aware!

gene_color | Merge Genes with Color Information Based on Up/Down Regulation
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 Colors and Transparency
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 rugs, and contours
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
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 Counts
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 Test