# Visualization and Integrated System for Transcriptomic Analysis

## Documentation for package ‘VISTA’ version 1.1.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E G M N P R S U V misc

## -- A --

as_deseq_dataset | Convert a VISTA object to a DESeqDataSet
as_vista | Coerce SummarizedExperiment to VISTA

## -- B --

benchmark_vista_equivalence | Benchmark VISTA against standalone differential-expression backends

## -- C --

comparisons | Accessor Methods for VISTA Object
comparisons-method | Accessor Methods for VISTA Object
counts | Raw counts from a VISTA object
counts-method | Raw counts from a VISTA object
count_data | Example RNA-seq count matrix shipped with VISTA
create_vista | Create a VISTA Object with Internal DE Analysis
cutoffs | Accessor Methods for VISTA Object
cutoffs-method | Accessor Methods for VISTA Object

## -- D --

deg_summary | Accessor Methods for VISTA Object
deg_summary-method | Accessor Methods for VISTA Object
derive_vista_metadata | Derive starter sample metadata from count sample names

## -- E --

enrichMsigDB | Perform MSigDB over-representation analysis on a VISTA object
enrichMsigDB-method | Perform MSigDB over-representation analysis on a VISTA object
example_vista | Build a small example VISTA object
export_vista_assets | Export a complete VISTA asset bundle

## -- G --

get_celltype_barplot | Plot cell-type composition as stacked bars
get_celltype_group_dotplot | Plot group-level deconvolution scores as dot plot
get_celltype_heatmap | Plot cell-type deconvolution heatmap
get_cell_fractions | Retrieve stored cell fraction estimates
get_corr_heatmap | Draw a sample correlation heatmap
get_deg_alluvial | Plot alluvial diagram showing gene regulation transitions across comparisons
get_deg_count_barplot | Barplot of DEG counts (Up/Down) across comparisons
get_deg_count_donutplot | Donut chart of DEG counts (Up/Down) across comparisons
get_deg_count_pieplot | Pie chart of DEG counts (Up/Down) across comparisons
get_deg_venn_diagram | DEG Venn diagram
get_enrichment_chord | Chord diagram of enrichment gene-pathway relationships
get_enrichment_plot | Plot enrichment results using -log10(FDR)
get_expression_barplot | Plot gene expression as barplots
get_expression_boxplot | Plot gene expression distributions as boxplots
get_expression_chromosome_plot | Chromosome plot for expression
get_expression_density | Plot expression distributions as density curves
get_expression_heatmap | Expression heatmap
get_expression_joyplot | Plot expression distributions as ridgelines
get_expression_lineplot | Gene expression line plot
get_expression_lollipop | Plot expression as a lollipop chart
get_expression_matrix | Retrieve an expression matrix from a VISTA object
get_expression_raincloud | Raincloud plot of expression values
get_expression_scatter | Compare normalized expression between two samples or groups
get_expression_violinplot | Violin plot of expression values
get_foldchange_barplot | Plot fold-change barplots across comparisons for selected genes
get_foldchange_boxplot | Plot fold-change distributions across comparisons
get_foldchange_chromosome_plot | Chromosome plot for fold change
get_foldchange_heatmap | Fold-change heatmap
get_foldchange_lineplot | Fold-change line plot across comparisons
get_foldchange_lollipop | Fold-change plotting helpers (overview)
get_foldchange_matrix | Extract a log2 fold-change matrix
get_foldchange_raincloud | Raincloud plot of fold-change distributions across comparisons
get_foldchange_scatter | Fold-change scatterplot between two comparisons
get_genes_by_regulation | Get Genes by Regulation
get_go_enrichment | Run GO enrichment directly from a VISTA comparison
get_gsea | Gene set enrichment analysis (GSEA) from a VISTA comparison
get_kegg_enrichment | Run KEGG enrichment directly from a VISTA comparison
get_ma_plot | Generate MA plot from a VISTA object
get_mds_plot | Generate an MDS plot for samples in a VISTA object
get_msigdb_enrichment | Run MSigDB enrichment directly from a VISTA comparison
get_pairwise_corr_plot | Plot pairwise correlations between samples
get_pathway_genes | Extract genes from enriched pathways
get_pathway_heatmap | Plot pathway-specific expression heatmaps from enrichment output
get_pca_plot | PCA plot
get_umap_plot | Generate a UMAP plot for samples in a VISTA object
get_volcano_plot | Generate a volcano plot for a comparison in a VISTA object
group_colors | Accessor Methods for VISTA Object
group_colors-method | Accessor Methods for VISTA Object
group_palette | Accessor Methods for VISTA Object
group_palette-method | Accessor Methods for VISTA Object

## -- M --

match_vista_inputs | Match count and metadata inputs for VISTA

## -- N --

norm_counts | Accessor Methods for VISTA Object
norm_counts-method | Accessor Methods for VISTA Object

## -- P --

print.VISTA | Print a VISTA object

## -- R --

read_vista_counts | Read and standardize count inputs for VISTA
read_vista_metadata | Read and standardize sample metadata for VISTA
row_data | Accessor Methods for VISTA Object
row_data-method | Accessor Methods for VISTA Object
run_cell_deconvolution | Run Cell Deconvolution on Bulk RNA-seq from VISTA Object
run_deseq_analysis | Run Differential Expression Analysis with DESeq2, edgeR, or limma-voom
run_edger_analysis | Run Differential Expression Analysis with DESeq2, edgeR, or limma-voom
run_limma_analysis | Run Differential Expression Analysis with DESeq2, edgeR, or limma-voom
run_vista_report | Generate a publication-ready VISTA workflow report

## -- S --

sample_info | Accessor Methods for VISTA Object
sample_info-method | Accessor Methods for VISTA Object
sample_metadata | Sample metadata accompanying the VISTA airway example counts
save_vista_data | Save VISTA tabular outputs to disk
save_vista_plot | Save a VISTA plot object to disk
set_de_source | Set active DE source in a VISTA object
set_rowdata | Set or append rowData annotations on a VISTA object
set_vista_comparison_colors | Set manual comparison colors in a VISTA object
set_vista_group_colors | Set manual group colors in a VISTA object
show-method | Display a VISTA object

## -- U --

updateObject-method | Update a VISTA object to the current metadata schema

## -- V --

validate_vista | Validate a VISTA object
validate_vista_deep | Deep validation of VISTA differential-expression fidelity
VISTA | VISTA S4 Class Definition
VISTA-accessors | Accessor Methods for VISTA Object
VISTA-class | VISTA S4 Class Definition
VISTA-deprecated | Deprecated and defunct arguments in VISTA
VISTA-show | Display a VISTA object
VISTA-subset | Subset a VISTA object

## -- misc --

[-method | Subset a VISTA object