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 |