Man pages for theMILOlab/cypro
A Toolbox for Analysis of Single Cell Microscopy Data
| addClusterVariables | Add discrete/categorical variables that group the cells |
| add_family | dummy |
| add_helper | Add helping text |
| addHierarchicalClusterVariables | Add hierarchical clustering results to overall data |
| addKmeansClusterVariables | Add kmeans clustering results to overall data |
| addPamClusterVariables | Add PAM clustering results to overall data |
| addStatVariables | Add numeric variables |
| add_vardenotation_to_cypro_object_shiny | Adds variable denotation from pdl to object |
| addVariableSet | Add predefined set of variables |
| adjustableDefaultInstructions | Valid default arguments |
| adjustDefaultInstructions | Adjust object based default |
| adjust_well_roi_vec | Function to make well roi vectors compatible with cypros... |
| adjust_well_vec | Function to make well vectors compatible with cypros... |
| agglomerateHierarchicalCluster | Agglomerate hierarchical cluster |
| allColorpalettes | Valid colorpanels & -spectra |
| animateAllTracks | Animate all tracks |
| animateWellImage | Animate cellular movement |
| argument_dummy | argument_dummy |
| assemble_additional_data_variables_module_info_shiny | Title |
| assemble_analysis_module_info_shiny | Title |
| assemble_id_module_info_shiny | Title |
| assemble_tracks_one_time_imaging_shiny | Integrate cell stat tables |
| assemble_tracks_time_lapse_shiny | Integrate cell track tables |
| assign_default | Assigns default to parent function |
| check_availability | Check content availability |
| check_df_variables | Detect missing variables |
| check_nrow | Detect poorly added variables |
| check_object | Check object input |
| check_phase | Check phase input |
| check_phase_manually | Check that phase is specified manually |
| checkpoint | Shiny feedback messages |
| check_renamed_variables | Detect protected variables |
| check_set_up_progress | Title |
| check_summarize_with | Input check of summarize_with |
| check_track_df | Check track data.frame |
| check_wp_df_shiny | Check well plate data.frame (shiny) |
| check_wp_directories | Detect double directories |
| check_wp_name | Check well plate name |
| cluster_df_descr | cluster_df |
| complete_tracks | Completes track data.frame: |
| compute_cell_stats | Summarize tracking data |
| compute_distance | Compute the distance between to points |
| computeDistanceMatrices | Compute distance matrices |
| compute_distances_from_origin | Compute the distances from origin |
| computeKmeansCluster | Compute cluster with kmeans |
| compute_migration_efficiency | Calculate migration efficiency |
| compute_module_variables | Compute module based variables |
| compute_n_missing_values | Compute n missing values |
| computePamCluster | Compute cluster with partitioning around medoids (PAM) |
| correlateAll | Compute correlation between variables |
| css_status | Return css status |
| designExperiment | Object initiation: Step 1 |
| detectBatchEffects | Detect batch effects |
| detectOutliers | Detect outlier cells |
| detect_outliers_iqr | Outlier detection functions |
| dim_red_df | dim_red_df |
| discardClusterVariables | Discard unwanted variables from your data |
| discardDistanceMatrix | Discard calculated distance matrix |
| discardStatVariables | Discard unwanted variables from your data |
| evaluate_file_availability_shiny | Evaluate the availability of files |
| example_selected | Title |
| existOutlierResults | Logical Tests |
| filterTracks | Filter track data.frame |
| getBatchEffectDf | Obtain batch effect computation results |
| getCellIds | Get cell ids |
| getCellLines | Obtain cell line and condition names |
| getCorrConv | Obtain cypros correlation objects |
| getData | Obtain data slots |
| getDataFrame | Obtain data.frame |
| get_dim_red_obj | Title |
| getGroupingDf | Obtain grouping information |
| getGroupingOptions | Obtain names of variables that group the cells |
| getGroupingVariableNames | Obtain grouping variable names of cell data |
| getGroupNames | Obtain group names a grouping variable contains |
| getHclustConv | Obtain cypros clustering objects |
| getHclustObj | Obtain the original clustering objects |
| getMissingValuesDf | Obtain missing value counts |
| getOutlierResults | Obtain outlier detection results |
| getOutlierWells | Obtain possible outlier wells |
| getPcaConv | Obtain dimensional reduction objects |
| getSetUpDf | Obtain well plate set up |
| getStatsDf | Obtain stat data.frame |
| getStatVariableNames | Obtain numeric variables of cell data |
| getStorageDirectory | Obtain storage directory |
| getTracksDf | Obtain track data.frame. |
| getVariableDf | Obtain variable centered summaries |
| getVariableSet | Obtain defined sets of variables |
| getVariableValues | Obtain variable overview |
| getWellPlateNames | Obtain well plate names |
| ggplot_family | Title |
| ggplot_return | ggplot_return |
| ggpubr_comparison_list | Prepare input for 'ggpubr::stat_compare_means()' |
| hlpr_add_data_to_cluster_object | Adds data to cluster object |
| hlpr_add_variable_specific_args | Complete argument list in compute_module_variables |
| hlpr_add_vset_suffix | Add variable set suffix |
| hlpr_assemble_df | Joins cell data with well plate meta data |
| hlpr_assemble_directory | Assemble a directory |
| hlpr_caption_add_on | Clarifying caption |
| hlpr_coords_flip_add_on | ggplot2 add on helpers |
| hlpr_create_meta_data | Create Cell Meta Data |
| hlpr_create_track_list | Process Track Data.frame |
| hlpr_glue_phase | Adjust phase input for feedback messages |
| hlpr_keep_messages | Selects or discards messages from lists within purrr::keep() |
| hlpr_merge_conditions | Merge conditions |
| hlpr_module_name_pairs | Returns a vector of names in example named by the actual... |
| hlpr_order_input | Work around |
| hlpr_phase_vertical_line | Add vertical phase separating line to lineplot |
| hlpr_pretty_colnames | Make pretty column names |
| hlpr_process_tracks | Processing helper |
| hlpr_rename_df_cols | Rename cell tracker columns |
| hlpr_select_stats | Where do I need this? |
| hlpr_split_subset | Split subset input |
| hlpr_subset_across | Subset the across-variables |
| hlpr_wp_directories | Return directory of well plate |
| hs | Horizontal Separation (width = 3) |
| initiateCorrelation | Set up correlation with cypro |
| initiateEmptyCyproObject | Initiate empty cypro object |
| initiateHierarchicalClustering | Set up clustering objects with cypro |
| input_df | input_df |
| is_modified_wp_df | Well plate data.frame check |
| labelsXrotate | Manipulate labels of ggplot output |
| legendBottom | Specify legend position of ggplot output |
| loadDataFile | Object initiation: Step 2 |
| load_data_files_shiny | Read in cell track data |
| loading_status_table_shiny | Display loading status |
| moduleExperimentDesignServer | Server logic: Experiment Design |
| moduleExperimentDesignUI | UI logic: Experiment Set Up |
| moduleLoadDataFileServer | Server logic: Load Data |
| moduleLoadDataFileUI | UI logic: Load Data |
| moduleLoadDataServer | Server logic: Load Data |
| moduleLoadDataUI | UI logic: Load Data |
| moduleQualityCheckServer | Server logic: Quality Check |
| moduleQualityCheckUI | UI logic: Quality Check |
| mutateClusterDf | Create and modify data variables |
| mutateTracksDf | Create and modify data variables |
| nCells | Number of miscellaneous content |
| nFiles | Number of files read in |
| nMissingValuesStats | Number of NAs by cell id (in stats) |
| nMissingValuesTracks | Number of NAs by cell id (in tracks) |
| normalizeZscore | Normalize data with zscore |
| plotAllTracks | Plot scaled cell migration |
| plotAvgSilhouetteWidths | Plot pam cluster quality |
| plotBarchart | Plot distribution of discrete variables |
| plotBatchHeatmap | Visualize possible batch effects |
| plotBoxplot | Plot numeric distribution and statistical tests |
| plotCellCount | Plot cell count |
| plotCorrelationSD | Plot correlation variance across groups |
| plotCorrplot | Plot a correlation plot |
| plotDendrogram | Visualize hierarchical clustering |
| plot_dim_red | Title |
| plotDimRed | Plot dimensional reduction |
| plotDistribution | Plot descriptive statistics |
| plotDistributionDiscrete | Distribution of discrete features |
| plotHeatmap | Plot numeric variables in a heatmap |
| plotPamMedoids | Plot medoid results |
| plotPca | Plot dimensional reduction results |
| plot_qc_barplot_shiny | Quality check barplot |
| plot_qc_histogram_shiny | Quality check histogram |
| plotScatterplot | Plot a scatterplot |
| plotScreeplot | Plot a scree plot |
| plotSingleTracks | Plot single cell migration |
| plotStatisticsInteractive | Plot statistics related plots interactively |
| plotTimeHeatmap | Visualize changes of cell characteristics over time |
| plotTimeLineplot | Visualize changes of cell characteristics over time |
| plotVelocityLineplot | Plot cell activity over time |
| plotWellPlate | Plot the well plate set up |
| plot_well_plate_shiny | Visualize the well plate |
| printSubsetHistory | Print subset information |
| printSummary | Print object summary |
| processData | Object initiation: Step 3 |
| protectedVariables | Protected variables |
| quality_check_summary_shiny | Summarize tracking quality |
| read_data_files_shiny | Reads cell track data |
| read_example_file_shiny | Read example file |
| read_table_shiny | wrapper around several table reading functions |
| removeOutliers | Remove outliers from object |
| renameClusterDf | Rename cluster variables |
| renameGroups | Rename groups |
| renameMetaDf | Rename meta variables |
| renameStatsDf | Rename statistic variables |
| renameTracksDf | Rename track variables |
| run_dim_red | Title |
| runPca | Compute dimensional reductions |
| saveCyproObject | Save cypro object |
| setCellDf | Set cell data.frame |
| setClusterConv | Set analysis objects |
| setDefaultInstructions | Set cypro default |
| setGroupingDf | Set data data.frames |
| setStorageDirectory | Set default storage directory |
| set_up_vdata | Computes variable summaries |
| setUpWellPlateDf | Create data.frame representing a well plate |
| shiny_fdb | Show shiny - notifications |
| starts_with | Imported selection helpers from package 'tidyselect' |
| subsetByCellId | Create data subset by cell ids |
| subsetByCellLine | Create data subset by cell lines |
| subsetByCluster | Create data subset by cluster |
| subsetByCondition | Create data subset by conditions |
| subsetByFilter | Create data subset by specified requirements |
| subsetByNumber | Create data subset by reducing the number of cells |
| subsetByQuality | Create data subset according to coverage quality |
| summarizeTrackDfWith | Summarize time lapse data variables |
| update_condition | Title |
| updateCyproObject | Keep cypro object up to data |
| updated_object | dummy |
| used_variable_names_shiny | Title |
| validAgglomerationMethods | Valid input options |
| validate_additional_variables_shiny | Title |
| validate_analysis_module_variables_shiny | Title |
| validate_identifier_variables_shiny | Title |
| valid_example_cols | Title |
| variables_num | Title |
