Analysis and Visualization of Multi-Omics Data

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Documentation for package ‘TransProR’ version 1.0.3

• 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