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IFC (version 0.2.1)

Tools for Imaging Flow Cytometry

Description

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository . See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

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Version

Install

install.packages('IFC')

Monthly Downloads

283

Version

0.2.1

License

GPL-3

Maintainer

Yohann Demont

Last Published

September 13th, 2023

Functions in IFC (0.2.1)

Batch Generation of Graphical and Statistic Report

ExportToGallery

CreateGraphReport

Graph Report Generation

Gallery Display

DAF File Writer

FCS File Writer

Batch File Writer

BatchStatsReport

Batch Generation of Statistic Report

Graphical and Statistic Report Display

RIF/CIF File Reader

ExtractImages_toFile

Shortcut for Batch Images Extraction to Files

Graphical and Statistic Report Generation

ExtractImages_toBase64

Shortcut for Batch Images Extraction to Base64

RIF/CIF File Writer

ExtractImages_toMatrix

Shortcut for Batch Images Extraction to Matrices/Arrays

DAF File Reader

FCS File Reader

FCS_merge_dataset

FCS Object Data Sets Merging

ExtractMasks_toMatrix

Shortcut for Batch Masks Extraction to Matrices/Arrays

Image Scale Bar Incrustation

Image Text Incrustation

Statistical Report Generation

FCS_check_keywords

FCS Keyword Checker

RIF/CIF File Conversion to TIFF

IFC Feature Coercion

base_axis_constr

Axis Constructor

FCS_merge_sample

FCS Object Samples Merging

ExtractMasks_toBase64

Shortcut for Batch Masks Extraction to Base64

base_hist_constr

Histogram Constructor for 'base' Plot

Character Color Check and RGB Conversion

`IFC_data` Object Check

IFC Statistics Coercion

Automatic Parameters Detection for IFC Graphs

Image Field Directory Builder

IFC Graph Coercion

buildPopulation

IFC Population Coercion

Raw Images to Base64 Encoding

2D Binned Kernel Density Estimation

cpp_base64_encode

Raw to Base64 Conversion

IFC Files Checksum

ExtractMasks_toFile

Shortcut for Batch Masks Extraction to Files

DAF File Checksum

Tools for Imaging Flow Cytometry

Apply Transformation

Use Rcpp for Range

FCS Object Converter

Raw Vectors Collapse

cpp_fast_rowAny

Use Rcpp to Apply Any on Matrix Rows

IFC Graph Adjustment

Checksum for RIF/CIF

RIF/CIF File Checksum

Integer to Hexadecimal Color Conversion

Assert that Certain Conditions are Met

Image Gamma Computation

Matrix Cropping

cpp_fast_listAny

Use Rcpp to Apply Any on List members

cpp_fast_factor

Fast Factorize Vector

applyGatingStrategy

Apply Gating Strategy

Matrix Cleanser

IFC Image Coercion

cpp_getoffsets_noid

IFC_offsets Computation without Id Determination

IFC Mask Coercion

IFC Region Coercion

cpp_as_nativeRaster

Image to Native Raster Conversion

Input Parameters Assertive Tool

IFC_object Extraction

Matrix HSV to RGB Conversion

Spatial Offsets Image Correction

Matrix Resizing

Draw Shape to Image

convert_spillover

Spillover Converter

Ellipse Boundaries to Coordinates

User's Coordinates to Pixels Conversion

Matrix to Matrix Writer According to Mask with Offsets

cpp_computeGamma

Gamma Computation

IFC_object Decompression

Equal Sized Matrix to Matrix Writer According to Mask

data_add_features

Add Feature to IFC_data Object

cpp_replace_non_finite

Non Finite Values Replacement

cpp_getoffsets_wid

IFC_offsets Computation with Object Identification

IFC_object Decompression to RAW

Multiple Pattern Fixed Matching

cpp_int32_to_uint32

Int32 to Uint32 32bits Conversion

Data Frame Merge Groups with Rcpp

cpp_v_int32_to_uint32

Vectorize Int32 to Uint32 32bits Conversion

Matrix Normalization

IFD Fast Tags Extraction

cpp_uint64_to_int64

Uint64 to Int64 64bits Conversion

cpp_uint32_to_raw

Uint32 to Raw Conversion

Combine by Columns

cpp_int64_to_uint64

Int64 to Uint64 64bits Conversion

Remove Population from an IFC_data Object

data_rm_regions

Remove Region from an IFC_data Object

cpp_offset_to_raw

Offset to Raw Conversion

Statistics Extraction

fromXML2_gating

GatingML Conversion from XML2

File Path Placeholders Formatting

RIF/CIF Image Field Directories Extraction

cpp_v_int64_to_uint64

Vectorize Int64 to Uint64 64bits Conversion

Feature Values Computation

cpp_fast_sample

Use Rcpp for Sampling

List IFC features

cpp_coord_to_px

Coordinates to Pixels

ASSIST Database Extraction

Alternative Names Generator

IFD Tags Extraction

Get Current Compilation Bits Depth

data_add_graphs

Add Graphs to IFC_data Object

Hexadecimal to Integer Color Conversion

cpp_pnt_in_gate

cpp_get_bytes_order

Get Bytes Order

inv_smoothAsinh

Inverse Smooth Asinh Transformation

cpp_inv_smoothLinLog

Inverse Smooth LinLog Transformation with Rcpp

Scale Constructor for IFC Graphs Plotting

Statistics Extraction from Populations

data_add_pop_sample

Population Sampling

Matrix Transformation

data_rm_features

Remove Features from an IFC_data Object

Remove Graph from an IFC_data Object

XML Node List Expansion

escape_entities

XML Entities Protection

inv_smoothLinLog

Inverse Smooth LinLog Transformation

Progress Bar Terminator

Colors for Smooth Density Plots

cpp_raw_to_offset

Offset to Raw Conversion

getImagesValues

RIF/CIF Image Values Extraction

File Extension Retrieval

Report Layout Extraction

Aborted Batch Files Retrieval

Parse Transformation Information

Histogram Smooth Constructor

Progress Bar Initializer

FCS Name Parser

Plot and Stats Computation for IFC Graph

DAF File Writer

data_add_regions

Add Region to IFC_data Object

Add Population to IFC_data Object

cpp_smoothLinLog

Smooth LinLog Transformation with Rcpp

AST File Writer

Sequence of Strings Matching

cpp_uint32_to_int32

Uint32 to Int32 32bits Conversion

IFC_pops Population Level Ordering

Feature Default Name Computation

RIF/CIF File Image Field Directories Offsets Extraction

Image Field Directory Full Tag Retrieval

IFC File Information Extraction

Seed Instructions Extraction

data_modify_pops

Modify Populations within IFC_data Object

Luminance Computation

data_modify_regions

Modify Populations within IFC_data Object

get_coordmap_raw

Device Raw Coordinates

get_coordmap_adjusted

Device Adjusted Coordinates

getFeaturesValues

Features Values Extraction

Populations Renaming

Histogram Constructor

Statistics Report Template Extraction

String Sequence Replacement

Object Extraction Parameters Definition

IFC_pops Computation

Object Cleanser

Lattice Histogram Panel Contructor

Object Colorizer

FCS Header Parser

readFCSdelimiter

FCS Delimiter Reader

popsRetrieveGraph

Graph Retrieval from Graphical IFC_pops

IFC_pops Checker for Object Membership to Populations

objectNormalize

Object Intensity Normalization

Object Extraction

popsGetObjectsIds

IFC_pops Object Numbers

redefine_features_def_feat

IFC_features_def Feature Redefinition

redefine_features_def

IFC_features_def Redefinition

FCS Data Parser

Lattice Key Panel Contructor

IFC_pops Levels Dependency Determination

Shortcut for Batch Images or Masks Extraction

Smooth LinLog Transformation

IFC_offset Subsetting

Numeric to String Formatting

redefine_masks_image

IFC_masks Image Redefinition

FCS Dataset Parser

Object File Export

Object Resizing

Special Character Replacement

Next Component Prediction

R/IDEAS Color Palette Mapping

IFC_pops Network Display

popsGetSiblings2

IFC_pops Sibling Population from Same Region Identification

redefine_masks_mask

IFC_masks Mask Redefinition

`IFC_plot` Conversion to 'raster' Plot

`IFC_plot` Statistics Extraction

Name Protection

readGatingStrategy

Gating Strategy File Reader

IFC_features_def Definition Splitting

Histogram y-Axis Limits Constructor

IFC Files Generic Reader

RIF/CIF File Subsetting

Random Name Generator

`IFC_plot` Conversion to 'base' Plot

Groups Combination

String Decomposition with Operators

toXML2_boolpop_gs

Boolean Population GatingML Conversion to XML2

String Decomposition with Placeholders

Change Graphs Layout

First Letter Only Capitalization

IFC_data Redefinition

File Path Decomposition

RIF/CIF File Merging

`IFC_plot` Conversion to 'lattice' Plot

Copy Populations from One File to Another File

Image Gamma Modification

String Truncation

Ellipsoid Polygon Constructor

IFC_images XML Conversion

tryReportFileCreation

Report File Creation

objectTransform

Object Transformation

IFC_graphs XML Conversion

toXML2_features

IFC_features XML Conversion

IFC_masks XML Conversion

popsGetAffiliation

IFC_pops Affiliation Finder

FCS File Parser

IFC_pops XML Conversion

popsGetSiblings1

IFC_pops Sibling Population from Same Base Identification

IFC Files Generic Writer

popsGetSiblings

IFC_pops Sibling Population Identification

Boolean Expression Validation

writeGatingStrategy

Gating Strategy File Writer

redefine_features_def_msk_img

IFC_features_def Mask or Image Redefinition

Histogram Val Constructor

IFC_regions XML Conversion

IFC_data Default Naming

FCS Text Parser

RIF/CIF Image Order Test

List to XML Conversion

IFC_masks Redefinition

Histogram Type Constructor

Smooth Asinh Transformation

Progress Bar Updater

Image Field Directory Writer

GatingML File Reader

toXML2_graphs_gs

IFC_graphs GatingML Conversion

IFC_images Raw Conversion

Text to Image Conversion

File Extension Removal

toXML2_graphpop_gs

Graphical Population GatingML Conversion to XML2

XML Node to List Conversion

IFC_features Raw Conversion

toXML2_spillover_gs

Spillover GatingML Conversion

IFC_stats XML Conversion

toXML2_features_def

IFC_features_def XML Conversion

List to XML Node Conversion

With Seed Evaluation

Input Identification