Vizualization tools for 'omics' datasets with R

Documentation for package ‘omXplore’ version 1.1.0

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-- 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.