Package index • smew

App creation

create_smew_app(): Preprocesses data and creates files for SMEW app

Introductory tabs

IntroPanel_AnnoTabUI() IntroPanel_AnnoTabServer(): Presents metabolite annotations in an interactive table

IntroPanel_OverviewTabUI() IntroPanel_OverviewTabServer(): Overviews the structure and features of the SMEW app

IntroPanel_SpatialVisTabUI() IntroPanel_SpatialVisTabServer(): Visualises peaks and metadata spatially across samples

Bulk-level tabs

BulkPanel_QCTabUI() BulkPanel_QCTabServer(): Visualises bulk-level quality control

BulkPanel_DATabUI() BulkPanel_DATabServer(): Performs differential intensity analysis

BulkPanel_DASummaryTabUI() BulkPanel_DASummaryTabServer(): Visualises bulk differential intensity results

BulkPanel_ORATabUI() BulkPanel_ORATabServer(): Performs pathway over-representation analysis

BulkPanel_GRNTabUI() BulkPanel_GRNTabServer(): Infers metabolite peak covariation networks

BulkPanel_MultiCompareTabUI() BulkPanel_MultiCompareTabServer(): Performs and visualises multi-group comparisons

BulkPanel_MultiGRNTabUI() BulkPanel_MultiGRNTabServer(): Infers multi-omics covariation networks

Region-level tabs

RegionPanel_DimRedTabUI() RegionPanel_DimRedTabServer(): Applies and visualises dimensionality reduction

RegionPanel_VotingTabUI() RegionPanel_VotingTabServer(): Creates and visualises regions of interest using a voting scheme across multiple peaks

RegionPanel_HistologyTabUI() RegionPanel_HistologyTabServer(): Allows users to manually select regions of interest, optionally using histology images

RegionPanel_SpatialClustersTabUI() RegionPanel_SpatialClustersTabServer(): Performs and visualises spatially-informed clustering per sample

RegionPanel_SpatialSmoothingTabUI() RegionPanel_SpatialSmoothingTabServer(): Spatially smooths and denoises cluster labels across neighbouring spots

RegionPanel_ComparisonTabUI() RegionPanel_ComparisonTabServer(): Compares multiple regions and/or clusters

RegionPanel_DATabUI() RegionPanel_DATabServer(): Performs and visualises region-based differential analysis

RegionPanel_RadialDistanceTabUI() RegionPanel_RadialDistanceTabServer(): Analyses and visualises relationships between molecular intensity and distance from a region of interest

RegionPanel_GRNTabUI() RegionPanel_GRNTabServer(): Infers and visualises region-based covariation networks

Pixel-level tabs

PixelPanel_EnrichmentTabUI() PixelPanel_EnrichmentTabServer(): Performs and visualises spatial pathway enrichment analysis

PixelPanel_SVMTabUI() PixelPanel_SVMTabServer(): Identifies modules of spatially variable and colocalised metabolite peaks