Man pages for kueckelj/confuns
Convenience Functions
| across_an1 | across an1 dummy |
| across_an2 | across an2 dummy |
| across_options | Across input |
| across_picker_input | Picker inputs |
| across_vis1 | across vis1 dummy |
| across_vis2 | across vis2 dummy |
| adapt_reference | Adapt glue reference |
| addClusterVarsHclust | Add hierarchical cluster variables |
| addClusterVarsKmeans | Add kmeans cluster variables |
| addClusterVarsPam | Add PAM cluster variables |
| addGroupingVars | Add grouping variables |
| adjust_corr_mtr | Adjust correlation matrix |
| adjust_ggplot_params | Adjust ggplot parameters |
| adjust_sub_colors | Create sub cluster colors |
| agglomerateHierarchicalTrees | Agglomerate hierarchical trees |
| all_color_palettes | Color palette names |
| all_colorpanels | Deprecated |
| all_colorspectra | Deprecated |
| all_vars_discrete | Check data.frame variables |
| AnalysisAspect-class | The 'AnalysisAspect'-class |
| Analysis-class | The 'AnalysisAspect'-class |
| argument_dummy | Argument dummy |
| arrange_rows | Arrange rows |
| assemble_list | Assemble list of objects |
| assignDefault | S4 Default Assignment |
| assign_obj | Assign objects into the global environment |
| assign_pam_default | Title |
| bin_numeric_variable | Convert a numeric variable to a discrete one |
| call_flexibly | Construct a flexible function call |
| change_order_input | Change order input |
| check_across_subset | Subset the across-variables |
| check_across_subset_negate | Check across subset input |
| check_assign | Check assign input |
| check_data_frame | Check data.frame validity |
| check_df_variables | Data.frame variable check |
| check_directories | Check directory input |
| check_h_k | Check h and k input for hclust |
| check_ks | Check and adjust k |
| check_method_corr | Title |
| check_none_of | Overwrite check |
| check_no_overlap | Check no overlap |
| check_one_of | Check valid values |
| checkpoint | Shiny feedback messages |
| check_vector | Compare input to control input |
| circumference | Compute circle circumference |
| Classification-class | The 'Classification'-class |
| clrp_aaas | American Association for the Advancement - color palette |
| clrp_egr | Elena Grabis - color palette |
| clrp_jama | The Journal of the American Medical Association - color... |
| clrp_jco | Journal of Oncology - color palette |
| clrp_lo | Lancet Oncology - color palette |
| clrp_milo | MILO Research Group - color palette |
| clrp_nejm | New England Journal of Medicine- color palette |
| clrp_npg | Nature Publishing Group - color palette |
| clrp_sifre | Simon Frerich - color palette |
| clrp_uc | University of Chicago - color palette |
| Clustering-class | The 'Clustering'-class |
| ClusteringMethod-class | The 'ClusteringMethod'-class |
| colorpalettes | Color palettes |
| color_palettes_md | Manually defined palettes |
| color_vector | Get vector of colors |
| computeClusteringHclust | Compute 'hclust' objects |
| compute_clustering_kmeans | Iterate over kmeans |
| computeClusteringKmeans | Compute cluster with kmeans |
| compute_clustering_pam | Iterate over pam |
| computeClusteringPam | Compute cluster with pam |
| computeCorrelation | Compute correlation |
| computeDistanceMatrices | Compute distance matrices |
| computePCA | Compute PCA |
| computeTSNE | Compute TSNE |
| computeUMAP | Compute UMAP |
| corr_dummy | corr_dummy |
| Correlation-class | The 'Correlation'-class |
| corr_mtr_to_df | Convert correlation matrix to data.frame |
| create_progress_bar | Create a progress bar object |
| degr2rad | Convert radians to degrees |
| detectOutliers | Detect outliers |
| detect_outliers_iqr | Detect outliers with IQR |
| detectOutliersIQR | Detect outliers |
| detect_outliers_mahalanobis | Detect outliers with Mahalanobis |
| df | normal df_dummy |
| DimRed-class | The 'Clustering'-class |
| DimRedMethod-class | The 'DimRedMethod' class |
| DimRedPCA-class | The 'DimRedPCA' |
| DimRedTSNE-class | The 'DimRedTSNE' |
| DimRedUMAP-class | The 'DimRedUMAP' |
| discard_if | Discard values |
| discard_unnamed | Discard unnamed elements |
| error_handler | Return function |
| extract_feedback | Title |
| feedback_list | A named list of possible feedback messages |
| filter_genes | Search for genes |
| fit_curve | Curve fitting |
| gene_info_df | Collection of gene information |
| getAnalysisAspect | Obtain objects of class 'AnalysisAspect' |
| getAvgSilWidthsDf | Obtain average sil-width data |
| getClustering | Obtain 'Clustering' object |
| getClusteringHclust | Obtain object of class 'ClusteringHclust' |
| getClusteringKmeans | Obtain object of class 'ClusteringKmeans' |
| getClusteringPam | Obtain object of class 'ClusteringPam' |
| getClusterVarsHclust | Obtain cluster variables (hclust) |
| getClusterVarsKmeans | Obtain cluster variables (kmeans) |
| getClusterVarsPam | Obtain cluster variables (PAM) |
| getCorrDf | Obtain correlation data.frame |
| getCorrelation | Obtain 'Correlation' object |
| getCorrMtr | Obtain correlation matrix |
| getDendro | Obtain object of class 'dendro' |
| getDendroSegmentDf | Obtain dendrogram segments |
| getDf | Obtain object data |
| getDimRed | Obtain 'DimRed' object |
| getDistMtr | Obtain distance matrix |
| getEmbeddingDf | Obtain 'DimRed' embedding |
| get_gene_names | Obtain gene names |
| get_gene_synonyms | Obtain gene synonyms |
| getHclust | Obtain object of class 'hclust' |
| getKeyDf | Obtain empty data.frame |
| getKmeans | Obtain object of class 'kmeans' |
| getMedoidsDf | Obtain medoids from PAM clustering |
| getMetaNames | Obtain meta names |
| getMtr | Obtain data matrix |
| getOutlierIDs | Obtain outlier ids |
| getOutlierResults | Obtain outlier results |
| getPam | Obtain object of class 'pam' |
| getRcorr | Obtain object of class 'rcorr' |
| getResults | Obtain analysis results |
| getScaledDf | Obtain scaled data |
| getScaledMtr | Obtain scaled matrix |
| getSilWidthsDf | Obtain sil-width data |
| getVariableNames | Obtain variable names |
| ggplot2_dummy | ggplot2_dummy |
| ggpubr_comparison_list | Prepare input for 'ggpubr::stat_compare_means()' |
| give_feedback | Print feedback in console |
| glue_list_report | Glue a human readable list report |
| hclust_dummy | hclust_dummy |
| hello | Hello, World! |
| hlpr_order_input | Work around |
| hm | Print top n matrix rows and columns |
| hs | Horizontal Separation (width = 3) |
| html_breaks | Title |
| initiateAnalysis | Initiate analysis |
| initiateAnalysisAspect | Initiate analysis |
| initiateOutlierDetection | Set up 'OutlierDetection' object |
| is_any_of | Any input check |
| is_color | Check if elements in a character vector represent valid... |
| is_key_variable | Test key variable validity |
| is_list | List input check |
| is_named | Logical naming test |
| is_value | One dimensional input check |
| join_lists | Join two lists by their names |
| join_safely | Title |
| lazy_check_dummy | This is a text dummy. |
| legend_none | Legend location |
| lin_alg_dummy | Lin alg dummy |
| load_files | Load in all files at once |
| load_functions | Load in all functions |
| load_scripts | Load in all R scripts |
| logical_to_group | Convert lgl vars to factors |
| make_available | Assign objects to environments |
| make_capital_letters | Capitalizes all words of a string |
| make_facet_add_on | Make facet add on |
| make_pretty_df | Make a data.frame more aesthetically pleasing |
| make_pretty_dummy | Yolo |
| make_pretty_name | Make string aesthetically pleasing |
| make_trig_vec | Create trigonometric vectors |
| melt_rcorr | Melt 'rcorr' |
| mrename | Rename matrix in tidyverse style |
| normalize | Normalize numeric values |
| normalize_dummy | normalize_dummy |
| normalize_zscore | Zscore computation |
| one_peak | Fit a curve |
| OutlierDetection-class | The 'OutlierDetection'-class |
| OutlierDetectionIQR-class | The 'OutlierDetectionIQR'-class |
| OutlierDetectionMahalanobis-class | The 'OutlierDetectionMahalanobis'-class |
| OutlierDetectionMethod-class | The 'OutlierDetectionMethod'-class |
| plot_and_save | Plot saving wrapper |
| plotAvgSilWidths | Plot avg sil-width data |
| plot_barplot | Plot distribution of discrete/categorical variables |
| plotBoxplot | Plot boxplot |
| plot_categorical_statistics_shiny | Title |
| plotCorrplot | Plot correlation plot |
| plotDendrogram | Plot dendrograms |
| plot_density | Plot distribution and results of statistical tests |
| plotDensityplot | Plot densityplot |
| plot_descriptive_statistics_shiny | Plot descriptive statistics |
| plot_dot_plot_1d | Plot 1d dot plot |
| plot_dot_plot_2d | Plot 2d dot plot |
| plot_gsea_dot | Plot GSEA hypergeometric test |
| plotHistogram | Plot histogram |
| plot_mosaic | Plot mosaic plot |
| plotPCA | Plot PCA |
| plotRidgeplot | Plot ridgeplot |
| plot_scatterplot | Title |
| plotScatterplot | Plot a scatterplot |
| plotScreeplot | Plot a screeplot |
| plotSilWidths | Plot sil-width data |
| plot_statistics | Plot distribution and results of statistical tests |
| plot_statistics_interactive | Opens interactive application |
| plotTSNE | Plot TSNE |
| plotUMAP | Plot UMAP |
| plot_violin | Plot distribution and results of statistical tests |
| plotViolinplot | Plot violinplot |
| print_gene_info | Print gene information |
| process_and_shift_df | Process a data.frame A wrapper around 'check_df_variables',... |
| proj_py_install_pkgs | Install Python Packages into a Virtual Environment |
| proj_py_pkg_installed | Check if a Python Package is Installed |
| proj_py_pkgs | List Installed Python Packages |
| proj_py_use_venv | Use a Specific Python Virtual Environment |
| proj_setup | Set Up Project Directories with Optional Python Environment |
| pull_var | Pull var safely |
| pythagoras_theorem | Pythagoras theorem |
| rad2degr | Convert radian to degree |
| radius | Compute circle radius |
| renameKeyVariable | Rename key variable |
| rename_safely | Save wrapper around dplyr::rename() |
| rgx_lookahead | Create lookahead/-behind regex |
| scale_color_add_on | ggplot2 - color add on |
| scaleData | Scale data |
| scollapse | Collapse with glue::glue_collapse |
| select_columns | Wrapper around dplyr::select() |
| sequential_single_hue | Color spectra names |
| setAnalysisAspect | Set objects of class 'AnalysisAspect' |
| setData | Set data and key variables |
| set_data_hlpr | Set data helper |
| setInstruction | Set instruction |
| shiny_fdb | Show shiny - notifications |
| show_colors | Visualize colorpalettes and -spectra |
| slider_input_alpha | Slider inputs |
| statistics_facet_wrap | Facet wrap add on |
| statistics_geom_jitter | Geom jitter add on |
| statistics_tests | Stat compare means |
| str_extract_before | Extract string content with lookarounds |
| str_suggest_vec | Obtain string suggestions |
| synonyms_to_hgnc | Map gene synonyms to HGNC symbols |
| theme_statistics | Theme for statistic plots |
| unfactor | Wrapper around unfactor() |
| unique_safely | Wrapper around unique and levels |
| validColorPalettes | Valid color inputs |
| validInput | Obtain valid input options |
| variable_classes | Obtain names with classes |
| variable_classes2 | Obtain classes with names |
| verbose | verbose |
| vselect | Select vector with tidyselect functions |
| wrap_standalone | Regex for standalone detection of words |
| wrap_strings | Wrap all elements of a character vector |
