# Vizualization tools for 'omics' datasets with R

## Documentation for package ‘omXplore’ version 1.0.0

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

## Help Pages

A B C D E F G H I L M O P Q S V W

## -- A --

accessors | Accessors functions
addModules | Shiny modules used by 'omXplore'

## -- B --

boxPlot | Displays different intensity plots.
BuildColorStyles | Build color style for DT tables
buildGraph | Display a CC
Build_enriched_qdata | Builds enriched assay with cell metadata info
Build_X_CC | Convert to enriched MultiAssayExperiment

## -- C --

Check_List_consistency | Convert to enriched MultiAssayExperiment
Check_MSnSet_Consistency | Convert to enriched MultiAssayExperiment
Check_se_Consistency | Convert to enriched MultiAssayExperiment
Children | Quantitative metadata vocabulary for entities
color-legend | Color legend for DaparToolshed
colorLegend | Color legend for DaparToolshed
colorLegend_server | Color legend for DaparToolshed
colorLegend_ui | Color legend for DaparToolshed
Compute_CC | Convert to enriched MultiAssayExperiment
converters | Convert to enriched MultiAssayExperiment
convert_to_mae | Convert to enriched MultiAssayExperiment
corrMatrix | Displays a correlation matrix of the quantitative data of a numeric matrix.
corrmatrix | Displays a correlation matrix of the quantitative data of a numeric matrix.
customChart | Customised resetZoom Button of highcharts plots
customExportMenu | #' @title Customised contextual menu of highcharts plots
custom_metacell_colors | Color legend for DaparToolshed
CVDist | Variance plot

## -- D --

density-plot | Displays a correlation matrix of the quantitative data of a numeric matrix.
densityPlot | Displays a correlation matrix of the quantitative data of a numeric matrix.
df_to_mae | Convert to enriched MultiAssayExperiment
df_to_se | Convert to enriched MultiAssayExperiment
display.CC.visNet | Display a CC
ds-pca | Bar plot of missing values per lines using highcharter.
ds-view | Bar plot of missing values per lines using 'highcharter'.

## -- E --

ExtendPalette | Palette for samples.
external_app | External module example
extFoo1 | External module example
extFoo1_server | External module example
extFoo1_ui | External module example
extFoo2 | External module example
extFoo2_server | External module example
extFoo2_ui | External module example

## -- F --

FormatDataForDT | Constructs a dataset suitable to use with the module format_DT.
formatDT | formatDT_ui and formatDT_server
formatDT_server | formatDT_ui and formatDT_server
formatDT_ui | formatDT_ui and formatDT_server
format_DT | formatDT_ui and formatDT_server

## -- G --

GetCCInfos | Display a CC
GetColorsForConditions | Palette for samples.
GetMetacellTags | Quantitative metadata vocabulary for entities
GetPkgVersion | Package version
get_adjacencyMatrix | Accessors functions
get_adjacencyMatrix-method | Accessors functions
get_cc | Accessors functions
get_cc-method | Accessors functions
get_colID | Accessors functions
get_colID-method | Accessors functions
get_group | Accessors functions
get_group-method | Accessors functions
get_metacell | Accessors functions
get_metacell-method | Accessors functions
get_parentProtId | Accessors functions
get_parentProtId-method | Accessors functions
get_pkg_version | Accessors functions
get_pkg_version-method | Accessors functions
get_type | Accessors functions
get_type-method | Accessors functions
globals | Global variables

## -- H --

heatmapD | Displays a correlation matrix of the quantitative data of a numeric matrix.
heatmapForMissingValues | Displays a correlation matrix of the quantitative data of a numeric matrix.

## -- I --

intensity-plots | Displays different intensity plots.
is.listOf | Checks the class of a list's slots

## -- L --

listOfdf_to_mae | Convert to enriched MultiAssayExperiment
listOfLists_to_mae | Convert to enriched MultiAssayExperiment
listOfmatrix_to_mae | Convert to enriched MultiAssayExperiment
listOfMSnSet_to_mae | Convert to enriched MultiAssayExperiment
listOfSE_to_mae | Convert to enriched MultiAssayExperiment
listPlotModules | Shiny modules used by 'omXplore'
listShinyApps | Shiny modules used by 'omXplore'
list_to_se | Convert to enriched MultiAssayExperiment

## -- M --

MAE_Compatibility_with_Prostar_1x | Convert datasets exported by the package 'Prostar'
MAE_to_mae | Convert to enriched MultiAssayExperiment
matrix_to_mae | Convert to enriched MultiAssayExperiment
matrix_to_se | Convert to enriched MultiAssayExperiment
metacell.def | Quantitative metadata vocabulary for entities
MSnSet_to_mae | Convert to enriched MultiAssayExperiment
MSnSet_to_se | Convert to enriched MultiAssayExperiment
mv.heatmap | Displays a correlation matrix of the quantitative data of a numeric matrix.

## -- O --

omXplore-modules | Shiny modules used by 'omXplore'
omXplore_corrmatrix | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_corrmatrix_server | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_corrmatrix_ui | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_density | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_density_server | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_density_ui | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_heatmap | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_heatmap_server | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_heatmap_ui | Displays a correlation matrix of the quantitative data of a numeric matrix.
omXplore_intensity | Displays different intensity plots.
omXplore_intensity_server | Displays different intensity plots.
omXplore_intensity_ui | Displays different intensity plots.
omXplore_pca | Bar plot of missing values per lines using highcharter.
omXplore_pca_server | Bar plot of missing values per lines using highcharter.
omXplore_pca_ui | Bar plot of missing values per lines using highcharter.
omXplore_tabExplorer | Explore 'MultiAssayExperiment' objects.
omXplore_tabExplorer_server | Explore 'MultiAssayExperiment' objects.
omXplore_tabExplorer_ui | Explore 'MultiAssayExperiment' objects.
omXplore_variance | Variance plot
omXplore_variance_server | Variance plot
omXplore_variance_ui | Variance plot

## -- P --

palette | Palette for samples.
Parent | Quantitative metadata vocabulary for entities
pep_prot_CC | Display a CC
pkgs.require | Loads packages
plot-variance | Variance plot
plotCCJitter | Display a CC
plotPCA_Eigen | Bar plot of missing values per lines using highcharter.
plotPCA_Eigen_hc | Bar plot of missing values per lines using highcharter.
plotPCA_Ind | Bar plot of missing values per lines using highcharter.
plotPCA_Var | Bar plot of missing values per lines using highcharter.
Prostar-1x-compatible | Convert datasets exported by the package 'Prostar'

## -- Q --

QFeatures_to_mae | Convert to enriched MultiAssayExperiment
q_metadata | Quantitative metadata vocabulary for entities

## -- S --

SampleColors | Palette for samples.
SE_Compatibility_with_Prostar_1.x | Convert datasets exported by the package 'Prostar'
SE_to_mae | Convert to enriched MultiAssayExperiment
sub_R25 | Feature example data

## -- V --

vdata | Feature example data
view_dataset | Bar plot of missing values per lines using 'highcharter'.
view_dataset_server | Bar plot of missing values per lines using 'highcharter'.
view_dataset_ui | Bar plot of missing values per lines using 'highcharter'.
violinPlot | Displays different intensity plots.

## -- W --

wrapper_pca | Bar plot of missing values per lines using highcharter.