Man pages for gitdemont/IFC
Tools for Imaging Flow Cytometry
| addScaleBar | Image Scale Bar Incrustation |
| addText | Image Text Incrustation |
| adjustGraph | IFC Graph Adjustment |
| applyGatingStrategy | Apply Gating Strategy |
| applyTrans | Apply Transformation |
| assert | Assert that Certain Conditions are Met |
| autoplot | Automatic Parameters Detection for IFC Graphs |
| base64_decode | Base64 to Raw Decoding |
| base64_encode | Raw to Base64 Encoding |
| base_axes | 'IFC_plot' Base Axes Annotation |
| base_axis_constr | Axis Constructor |
| base_hist_constr | Histogram Constructor for 'base' Plot |
| base_key | 'IFC_plot' Base Legend Annotation |
| base_regions | 'IFC_plot' Base Regions Annotation |
| base_theme | 'IFC_plot' Base Theme Creation |
| base_title | 'IFC_plot' Base Title Annotation |
| base_xaxis | 'IFC_plot' Base x Axis Annotation |
| base_yaxis | 'IFC_plot' Base y Axis Annotation |
| BatchReport | Batch Generation of Graphical and Statistic Report |
| BatchStatsReport | Batch Generation of Statistic Report |
| buildBatch | Batch Builder |
| buildFeature | IFC Feature Coercion |
| buildGraph | IFC Graph Coercion |
| buildIFD | Image Field Directory Builder |
| buildImage | IFC Image Coercion |
| buildMask | IFC Mask Coercion |
| buildPopulation | IFC Population Coercion |
| buildRegion | IFC Region Coercion |
| buildStats | IFC Statistics Coercion |
| calcDensity | 2D Binned Kernel Density Estimation |
| checkColor | Character Color Check and RGB Conversion |
| checkObj | 'IFC_data' Object Check |
| checksumDAF | DAF File Checksum |
| checksumIFC | IFC Files Checksum |
| checksumXIF | RIF/CIF File Checksum |
| colConv | Integer to Hexadecimal Color Conversion |
| collapse_raw | Raw Vectors Collapse |
| computeGamma | Image Gamma Computation |
| convert_spillover | Spillover Converter |
| coord_to_px | User's Coordinates to Pixels Conversion |
| cpp_align | Spatial Offsets Image Correction |
| cpp_as_nativeRaster | Image to Native Raster Conversion |
| cpp_assert | Input Parameters Assertive Tool |
| cpp_base64_decode | Base64 to Raw Conversion |
| cpp_base64_encode | Raw to Base64 Conversion |
| cpp_cast_image | Cast Image |
| cpp_checksum | Checksum for RIF/CIF |
| cpp_checkTIFF | TIFF Checker |
| cpp_cleanse | Matrix Cleanser |
| cpp_computeGamma | Gamma Computation |
| cpp_coord_to_px | Coordinates to Pixels |
| cpp_crop | Matrix Cropping |
| cpp_decomp | IFC_object Decompression |
| cpp_draw | Draw Shape to Image |
| cpp_ell_coord | Ellipse Boundaries to Coordinates |
| cpp_extract | IFC_object Extraction |
| cpp_fast_factor | Fast Factorize Vector |
| cpp_fast_listAny | Use Rcpp to Apply Any on List members |
| cpp_fast_range | Use Rcpp for Range |
| cpp_fast_rowAny | Use Rcpp to Apply Any on Matrix Rows |
| cpp_fast_sample | Use Rcpp for Sampling |
| cpp_fastTAGS | IFD Fast Tags Extraction |
| cpp_getBits | Get Current Compilation Bits Depth |
| cpp_get_bytes_order | Get Bytes Order |
| cpp_getoffsets_noid | IFC_offsets Computation without Id Determination |
| cpp_getoffsets_wid | IFC_offsets Computation with Object Identification |
| cpp_getTAGS | IFD Tags Extraction |
| cpp_getversion | Get Current Package Version |
| cpp_group_df | Data Frame Merge Groups with Rcpp |
| cpp_int32_to_uint32 | Int32 to Uint32 32bits Conversion |
| cpp_int64_to_uint64 | Int64 to Uint64 64bits Conversion |
| cpp_inv_smoothLinLog | Inverse Smooth LinLog Transformation with Rcpp |
| cpp_mark | Matrix to Matrix Writer According to Mask with Offsets |
| cpp_mask | Equal Sized Matrix to Matrix Writer According to Mask |
| cpp_M_HSV2RGB | Matrix HSV to RGB Conversion |
| cpp_mpfmatch | Multiple Pattern Fixed Matching |
| cpp_normalize | Matrix Normalization |
| cpp_offset_to_raw | Offset to Raw Conversion |
| cpp_pnt_in_gate | Point in Gate |
| cpp_raster | Raster Image |
| cpp_rawdecomp | IFC_object Decompression to RAW |
| cpp_raw_to_offset | Offset to Raw Conversion |
| cpp_readchunk | File Raw Chunk Extraction |
| cpp_readFCS | FCS data extraction |
| cpp_replace_non_finite | Non Finite Values Replacement |
| cpp_resize | Matrix Resizing |
| cpp_scanFirst | File Scanner |
| cpp_seqmatch | Sequence of Strings Matching |
| cpp_smoothLinLog | Smooth LinLog Transformation with Rcpp |
| cpp_transform | Matrix Transformation |
| cpp_uint32_to_int32 | Uint32 to Int32 32bits Conversion |
| cpp_uint32_to_raw | Uint32 to Raw Conversion |
| cpp_uint64_to_int64 | Uint64 to Int64 64bits Conversion |
| cpp_v_int32_to_uint32 | Vectorize Int32 to Uint32 32bits Conversion |
| cpp_v_int64_to_uint64 | Vectorize Int64 to Uint64 64bits Conversion |
| cpp_writeBMP | BMP Writer |
| cpp_writeIFD | IFD Tag Writer |
| CreateGraphReport | Graph Report Generation |
| createOME | OME XML Writer |
| data_add_features | Add Feature to IFC_data Object |
| data_add_graphs | Add Graphs to IFC_data Object |
| data_add_pops | Add Population to IFC_data Object |
| data_add_pop_sample | Population Sampling |
| data_add_regions | Add Region to IFC_data Object |
| data_modify_pops | Modify Populations within IFC_data Object |
| data_modify_regions | Modify Populations within IFC_data Object |
| data_rm_features | Remove Features from an IFC_data Object |
| data_rm_graphs | Remove Graph from an IFC_data Object |
| data_rm_pops | Remove Population from an IFC_data Object |
| data_rm_regions | Remove Region from an IFC_data Object |
| data_to_AST | AST File Writer |
| data_to_DAF | DAF File Writer |
| densCols | Colors for Smooth Density Plots |
| dev_close | Graphical Devices Shutdown |
| DisplayGallery | Gallery Display |
| DisplayReport | Graphical and Statistic Report Display |
| editMetadata | Metadata Editor |
| editTag | Image Field Directory Tag Editor |
| endPB | Progress Bar Terminator |
| escape_entities | XML Entities Protection |
| expand_list | XML Node List Expansion |
| ExportToBATCH | Batch File Writer |
| ExportToDAF | DAF File Writer |
| ExportToFCS | FCS File Writer |
| ExportToGallery | Gallery Export |
| ExportToNumpy | Numpy Export |
| ExportToReport | Graphical and Statistic Report Generation |
| ExportToXIF | RIF/CIF File Writer |
| ExtractFromDAF | DAF File Reader |
| ExtractFromFCS | FCS File Reader |
| ExtractFromXIF | RIF/CIF File Reader |
| ExtractImages_toBase64 | Shortcut for Batch Images Extraction to Base64 |
| ExtractImages_toFile | Shortcut for Batch Images Extraction to Files |
| ExtractImages_toMatrix | Shortcut for Batch Images Extraction to Matrices/Arrays |
| ExtractImages_toMulti | Shortcut for Batch Images Extraction to Multichannel Tiff |
| ExtractMasks_toBase64 | Shortcut for Batch Masks Extraction to Base64 |
| ExtractMasks_toFile | Shortcut for Batch Masks Extraction to Files |
| ExtractMasks_toMatrix | Shortcut for Batch Masks Extraction to Matrices/Arrays |
| ExtractMasks_toMulti | Shortcut for Batch Masks Extraction to Multichannel Tiff |
| extractStats | Statistics Extraction |
| fastAny | Any with Rcpp |
| fastCbind | Combine by Columns |
| FCS_check_keywords | FCS Keyword Checker |
| FCS_merge_dataset | FCS Object Data Sets Merging |
| FCS_merge_sample | FCS Object Samples Merging |
| FCS_to_data | FCS Object Converter |
| featureIFC | List IFC features |
| feature_namer | Feature Default Name Computation |
| fetch_seed | Seed Instructions Extraction |
| formatdate | Date Converter |
| formatn | File Path Placeholders Formatting |
| fromXML2_gating | GatingML Conversion from XML2 |
| gen_altnames | Alternative Names Generator |
| getAborted | Aborted Batch Files Retrieval |
| getASSIST | ASSIST Database Extraction |
| get_coordmap_adjusted | Device Adjusted Coordinates |
| get_coordmap_raw | Device Raw Coordinates |
| getFeaturesValues | Features Values Extraction |
| get_feat_value | Feature Values Computation |
| getFileExt | File Extension Retrieval |
| getFullTag | Image Field Directory Full Tag Retrieval |
| getIFD | RIF/CIF Image Field Directories Extraction |
| getImagesValues | RIF/CIF Image Values Extraction |
| getInfo | IFC File Information Extraction |
| getloc | Get Locale |
| getLuminance | Luminance Computation |
| getOffsets | RIF/CIF File Image Field Directories Offsets Extraction |
| get_pops_stats | Statistics Extraction from Populations |
| getSTATSREPORT | Statistics Report Template Extraction |
| get_ylim | Histogram y-Axis Limits Constructor |
| group | Groups Combination |
| gseq | String Sequence Replacement |
| hist_constr | Histogram Constructor |
| IFC-package | Tools for Imaging Flow Cytometry |
| IFDtype | IFD Type Detection |
| inv_colConv | Hexadecimal to Integer Color Conversion |
| inv_smoothAsinh | Inverse Smooth Asinh Transformation |
| inv_smoothLinLog | Inverse Smooth LinLog Transformation |
| keep_attributes | Attributes Keeper |
| lattice_theme | 'IFC_plot' Lattice Theme Creation |
| layoutReport | Report Layout Extraction |
| map_color | Color Mapping |
| map_style | Style Mapping |
| mergeXIF | RIF/CIF File Merging |
| modifyGamma | Image Gamma Modification |
| myScales | Scale Constructor for IFC Graphs Plotting |
| newPB | Progress Bar Initializer |
| next_bool | Next Component Prediction |
| num_to_string | Numeric to String Formatting |
| objectCleanse | Object Cleanser |
| objectColorize | Object Colorizer |
| objectDisplay | Object Display |
| objectExtract | Object Extraction |
| objectNormalize | Object Intensity Normalization |
| objectParam | Object Extraction Parameters Definition |
| objectResize | Object Resizing |
| objectTransform | Object Transformation |
| objectWrite | Object File Export |
| paletteIFC | R/IDEAS Color Palette Mapping |
| pan_hist | Lattice Histogram Panel Contructor |
| pan_key | Lattice Key Panel Contructor |
| pan_smooth | Histogram Smooth Constructor |
| parseFCSname | FCS Name Parser |
| parseTrans | Parse Transformation Information |
| plot_backend | 'IFC_plot' Plotting |
| plot_base | 'IFC_plot' Conversion to 'base' Plot |
| plot_base_empty | 'IFC_plot' Base Empty Plot Creation |
| plot_base_error | Erroneous 'IFC_plot' Conversion to 'base' Plot |
| plot_default_args | 'IFC_plot' Default Arguments Computation |
| plotGraph | Plot and Stats Computation for IFC Graph |
| plot_lattice | 'IFC_plot' Conversion to 'lattice' Plot |
| plot_lattice_empty | 'IFC_plot' Lattice Empty Plot Creation |
| plot_lattice_error | Erroneous 'IFC_plot' Conversion to 'lattice' Plot |
| plot_raster | 'IFC_plot' Conversion to 'raster' Plot |
| plot_raster_empty | 'IFC_plot' Raster Empty Plot Creation |
| plot_raster_error | Erroneous 'IFC_plot' Conversion to 'raster' Plot |
| plot_stats | 'IFC_plot' Statistics Extraction |
| polyExtractTo | Shortcut for Batch Images or Masks Extraction |
| popsCompute | IFC_pops Computation |
| popsCopy | Copy Populations from One File to Another File |
| popsGetAffiliation | IFC_pops Affiliation Finder |
| popsGetLevels | IFC_pops Levels Dependency Determination |
| popsGetObjectsIds | IFC_pops Object Numbers |
| popsGetSiblings | IFC_pops Sibling Population Identification |
| popsGetSiblings1 | IFC_pops Sibling Population from Same Base Identification |
| popsGetSiblings2 | IFC_pops Sibling Population from Same Region Identification |
| popsNetwork | IFC_pops Network Display |
| popsOrderNodes | IFC_pops Population Level Ordering |
| popsRename | Populations Renaming |
| popsRetrieveGraph | Graph Retrieval from Graphical IFC_pops |
| popsWithin | IFC_pops Checker for Object Membership to Populations |
| pow2 | Power of Two |
| protectn | Name Protection |
| pseudo_seed | Pseudo Seed |
| random_name | Random Name Generator |
| rasterplot | Fast 2D plot |
| readFCS | FCS File Parser |
| readFCSdata | FCS Data Parser |
| readFCSdataset | FCS Dataset Parser |
| readFCSdelimiter | FCS Delimiter Reader |
| readFCSheader | FCS Header Parser |
| readFCStext | FCS Text Parser |
| readGatingML | GatingML File Reader |
| readGatingStrategy | Gating Strategy File Reader |
| readIFC | IFC Files Generic Reader |
| redefine_features_def | IFC_features_def Redefinition |
| redefine_features_def_feat | IFC_features_def Feature Redefinition |
| redefine_features_def_msk_img | IFC_features_def Mask or Image Redefinition |
| redefine_masks | IFC_masks Redefinition |
| redefine_masks_image | IFC_masks Image Redefinition |
| redefine_masks_mask | IFC_masks Mask Redefinition |
| redefine_obj | IFC_data Redefinition |
| relayout | Change Graphs Layout |
| remove_ext | File Extension Removal |
| rev_string | Reverse String |
| setloc | Set Locale |
| setPB | Progress Bar Updater |
| setupimage | Image Setup for TIFF Export |
| smoothAsinh | Smooth Asinh Transformation |
| smoothLinLog | Smooth LinLog Transformation |
| specialr | Special Character Replacement |
| splitf | File Path Decomposition |
| split_feat | IFC_features_def Definition Splitting |
| splitn | String Decomposition with Operators |
| splitp | String Decomposition with Placeholders |
| splits | Sync Name Decomposition |
| StatsReport | Statistical Report Generation |
| subsetOffsets | IFC_offset Subsetting |
| subsetXIF | RIF/CIF File Subsetting |
| swap_channel | Channel Swap |
| switch_channel | Channel Switch |
| testXIF | RIF/CIF Image Order Test |
| texttomatrix | Text to Image Conversion |
| toBIN_features | IFC_features Raw Conversion |
| toBIN_images | IFC_images Raw Conversion |
| toCapFirstOnly | First Letter Only Capitalization |
| toEllipse | Ellipsoid Polygon Constructor |
| to_list_node | XML Node to List Conversion |
| toXML2_boolpop_gs | Boolean Population GatingML Conversion to XML2 |
| toXML2_features | IFC_features XML Conversion |
| toXML2_features_def | IFC_features_def XML Conversion |
| toXML2_graphpop_gs | Graphical Population GatingML Conversion to XML2 |
| toXML2_graphs | IFC_graphs XML Conversion |
| toXML2_graphs_gs | IFC_graphs GatingML Conversion |
| toXML2_images | IFC_images XML Conversion |
| toXML2_masks | IFC_masks XML Conversion |
| toXML2_pops | IFC_pops XML Conversion |
| toXML2_regions | IFC_regions XML Conversion |
| toXML2_spillover_gs | Spillover GatingML Conversion |
| toXML2_stats | IFC_stats XML Conversion |
| to_xml_list | List to XML Node Conversion |
| trunc_string | String Truncation |
| tryReportFileCreation | Report File Creation |
| type_constr | Histogram Type Constructor |
| usedefault_obj | IFC_data Default Naming |
| val_constr | Histogram Val Constructor |
| validate_bool | Boolean Expression Validation |
| whoami | Input Identification |
| with_seed | With Seed Evaluation |
| wrap_label | Graphical Text Wrap |
| writeGatingStrategy | Gating Strategy File Writer |
| writeIFC | IFC Files Generic Writer |
| writeIFD | Image Field Directory Writer |
| writemulti | Tiff Writer |
| writetiff | Tiff Writer |
| XIFtoTIFF | RIF/CIF File Conversion to TIFF |
| xml_new_node | List to XML Conversion |
