Vizualization tools for 'omics' datasets with R
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Documentation for package ‘omXplore’ version 1.2.0
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 | my_PCA |
| 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_design | Accessors functions |
| get_design-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. |
| my_PCA | my_PCA |
-- 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 | my_PCA |
| omXplore_pca_server | my_PCA |
| omXplore_pca_ui | my_PCA |
| 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 | my_PCA |
| plotPCA_Eigen_hc | my_PCA |
| plotPCA_Ind | my_PCA |
| plotPCA_Var | my_PCA |
| 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 | my_PCA |