Man pages for kueckelj/celltracer
An Analysis-Toolbox for High-Throughput Cell Imaging Data
| across_dummy | across |
| addClusterVariable | Add discrete/categorical variables |
| addDimRedData | Add dimensional reduction data |
| add_family | dummy |
| add_on_list | add_on_list |
| aes_to | aes_to |
| allColorpanels | Valid colorpanels & -spectra |
| animateAllTracks | Title |
| animateWellImage | Animate cellular movement |
| argument_dummy | argument_dummy |
| assemble_track_df_shiny | Integrate cell track tables |
| cell_ids | cell_ids |
| check_cell_track_variables | Detect missing variables |
| check_object | dummy |
| check_pam_input | Check pam input |
| check_phase | Check phase input |
| checkpoint | Shiny feedback messages |
| check_pt | Title |
| check_smooth | Check smooth |
| 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 | cluster_df |
| colors | colors |
| compileCto | Compiles a cell tracer object |
| compute_distance | Compute the distance between to points |
| compute_distances_from_origin | Compute the distances from origin |
| compute_migration_efficiency | Calculate migration efficiency |
| compute_stat | Summarize tracking data |
| computeUmapData | Compute Umap data |
| dim_red_df | dim_red_df |
| dim_red_method | dim_red_method |
| doPamClustering | Title |
| evaluate_file_availability | Evaluate the availability of files |
| filterTracks | Filter track data.frame |
| getCellLines | Obtain cell line and condition names |
| getClusterData | Obtain cluster data |
| getClusterNames | Obtain valid cluster names |
| getData | Obtain data slots |
| getDimRed | Obtain dimensional reduction data |
| getGroupingOptions | Obtain variable names that group the cells |
| getGroupNames | Obtain group names a grouping variable contains |
| getMeta | Obtain meta data |
| getPamObject | Obtain pam-clustering results. |
| getStats | Obtain stat data.frame |
| getStatVariableNames | Obtain all numeric stat-variables |
| getTracks | Obtain track data.frame. |
| 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_assemble_directory | Assemble a directory |
| hlpr_assemble_track_df | Assemble a cell id |
| hlpr_caption_add_on | Clarifying caption |
| hlpr_coords_flip_add_on | ggplot2 add on helpers |
| hlpr_create_track_list | Process Track Data.frame |
| hlpr_order_input | Work around |
| hlpr_pretty_colnames | Make pretty column names |
| hlpr_rename_cell_track_cols | Rename cell tracker columns |
| hlpr_select_stats | Where do I need this? |
| hlpr_subset_across | Subset the across-variables |
| hlpr_wp_directories | Return directory of well plate |
| hs | Horizontal Separation (width = 3) |
| image | image |
| initiateCTO | Create a Cell Tracer Object |
| input_df | input_df |
| launchCellTracer | Access interactive application |
| linesize | linesize |
| linetype | linetype |
| load_cell_track_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 |
| moduleLoadDataServer | Server logic: Load Data |
| moduleLoadDataUI | UI logic: Load Data |
| moduleQualityCheckServer | Server logic: Quality Check |
| moduleQualityCheckUI | UI logic: Quality Check |
| n_cells | n_cells |
| phase_all | phase_all |
| phase_cluster | phase_cluster |
| phase_single | phase_single |
| plotAllTracks | Plot cell migration |
| plotBarchart | Plot distribution of discrete variables |
| plotBoxplot | Plot numeric distribution and statistical tests |
| plotCellCount | Plot cell count |
| plotDimRed | Plot dimensional reduction |
| plotDistribution | Plot descriptive statistics |
| plotDistributionDiscrete | Distribution of discrete features |
| plotPamClusterCount | Plot Number of Cells in Cluster |
| plotPamClusterSummary | Plot Cluster Summary |
| plotPamMedoidSummary | Plot Medoid/Cluster Information |
| plotPamSilWidth | Plot Cluster Quality |
| plot_qc_barplot_shiny | Quality check barplot |
| plot_qc_histogram_shiny | Quality check histogram |
| plotSingleTracks | Plot single cell migration |
| plotVelocityHeatmap | Plot cell velocity over time |
| plotVelocityLineplot | Plot cell activity over time |
| plotWellPlate | Plot the well plate set up |
| plot_well_plate_shiny | Visualize the well plate |
| pretty_names | pretty_names |
| pt_args | pt_args |
| quality_check_summary_shiny | Summarize tracking quality |
| read_ct_data_shiny | Reads cell track data |
| setUpWellPlateDf | Well Plate Data.frame |
| shiny_fdb | Show shiny - notifications |
| updated_object | dummy |
| variables_num | Title |
| verbose | variables_num |
| well | well |
| well_plate | well_plate |
| with_cluster | with_clsuter |
| with_meta | with_meta |
| with_stats | with_stats |
