Visualization and Integrated System for Transcriptomic Analysis

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Documentation for package ‘VISTA’ version 0.99.8

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

Help Pages

as_vista	Coerce SummarizedExperiment to VISTA
benchmark_vista_equivalence	Benchmark VISTA against standalone differential-expression backends
comparisons	Accessor Methods for VISTA Object
comparisons-method	Accessor Methods for 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
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
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
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
match_vista_inputs	Match count and metadata inputs for VISTA
norm_counts	Accessor Methods for VISTA Object
norm_counts-method	Accessor Methods for VISTA Object
print.VISTA	Print a VISTA object like a SummarizedExperiment
print.vista	Print a VISTA object like a SummarizedExperiment
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
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
validate_vista	Validate a VISTA object
validate_vista_deep	Deep validation of VISTA differential-expression fidelity
VISTA-accessors	Accessor Methods for VISTA Object
VISTA-class	VISTA S4 Class Definition