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IFC (version 0.1.1)

Tools for Imaging Flow Cytometry

Description

Contains several tools to treat imaging flow cytometry data from 'ImageStream' and 'FlowSight' cytometers ('Amnis', part of 'Luminex'). Provides an easy and simple way to read, write and subset .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved. 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 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

0.1.1

License

GPL-3

Maintainer

Yohann Demont

Last Published

December 18th, 2020

Functions in IFC (0.1.1)

RIF/CIF File Reader

Gallery Display

RIF/CIF File Writer

ExportToGallery

ExtractImages_toBase64

Shorcut for Batch Images Extraction to Base64

DAF File Writer

Batch File Writer

DAF File Reader

Graphical and Statistic Report Generation

ExtractImages_toFile

Shorcut for Batch Images Extraction to Files

Image Scale Bar Incrustation

Automatic Parameters Detection for IFC Graphs

Character Color Check and RGB Conversion

ExtractImages_toMatrix

Shorcut for Batch Images Extraction to Matrices/Arrays

ExtractMasks_toMatrix

Shorcut for Batch Masks Extraction to Matrices/Arrays

cpp_base64_encode

Raw to Base64 Conversion

Assert that Certain Conditions are Met

IFC Graph Adjustment

2D Binned Kernel Density Estimation

DAF File Checksum

IFC Graph Coercion

Tools for Imaging Flow Cytometry

IFC Feature Coercion

buildPopulation

IFC Population Coercion

Image Text Incrustation

IFC Files Checksum

Matrix HSV to RGB Conversion

Image Field Directory Builder

IFC_object Decompression

cpp_int32_to_uint32

Int32 to Uint32 32bits Conversion

Input Parameters Assertive Tool

cpp_inv_smoothLinLog

Inverse Smooth LinLog Transformation with Rcpp

Matrix Transformation

Checksum for RIF/CIF

IFC Region Coercion

Matrix Normalization

Raw Images to Base64 Encoding

Matrix Cleanser

RIF/CIF File Checksum

IFD Tags Extraction

Integer to Hexadecimal Color Conversion

IFC_object Extraction

cpp_uint32_to_int32

Uint32 to Int32 32bits Conversion

File Extension Retrieval

cpp_computeGamma

Gamma Computation

cpp_smoothLinLog

Smooth LinLog Transformation with Rcpp

base_axis_constr

Axis Constructor for 'base' Plot

cpp_num_to_string

Numeric to String Conversion

data_rm_regions

Remove Region from an IFC_data Object

Matrix to Matrix Writer According to Mask with Offsets

Ellipse Boundaries to Coordinates

Image Field Directory Full Tag Retrieval

DAF File Writer

escape_entities

XML Entities Protection

XML Node List Expansion

Matrix Cropping

base_hist_constr

Histogram Constructor for 'base' Plot

data_rm_features

Remove Features from an IFC_data Object

cpp_pnt_in_gate

Matrix Resizing

Equal Sized Matrix to Matrix Writer According to Mask

Remove Population from an IFC_data Object

IFC File Information Extraction

Luminance Computation

RIF/CIF File Merging

Image Gamma Computation

Image Gamma Modification

convert_to_baseplot

IFC Graph Conversion to 'base' Plot

Object Cleanser

Numeric to String Formatting

data_add_features

Add Feature to IFC_data Object

RIF/CIF File Image Field Directories Offsets Extraction

Aborted Batch Files Retrieval

File Path Placeholders Formatting

Copy Populations from One File to Another File

cpp_getoffsets_noid

IFC_offsets Computation without Id Determination

popsGetAffiliation

IFC_pops Affiliation Finder

Object Extraction

Object Extraction Parameters Definition

Histogram y-Axis Limits Constructor

cpp_getoffsets_wid

IFC_offsets Computation with Object Identification

Object Resizing

Add Population to IFC_data Object

Colors for Smooth Density Plots

IFC_pops Checker for Object Membership to Populations

Plot and Stats Computation for IFC Graph

objectNormalize

Object Intensity Normalization

Text to Image Conversion

RIF/CIF File Subsetting

Progress Bar Terminator

IFC_pops Computation

IFC_pops XML Conversion

Object Colorizer

R/IDEAS Color Palette Mapping

IFC_regions XML Conversion

popsRetrieveGraph

Graph Retrieval from Graphical IFC_pops

IFC_pops Network Display

IFC_graphs XML Conversion

popsGetSiblings2

IFC_pops Sibling Population from Same Region Identification

toXML2_features_def

IFC_features_def XML Conversion

IFC_pops Population Level Ordering

Lattice Histogram Panel Contructor

File Path Decomposition

XML Node to List Conversion

Name Protection

IFC Files Generic Writer

String Decomposition with Operators

Smooth LinLog Transformation

Special Character Replacement

List to XML Conversion

String Truncation

IFC_features Raw Conversion

IFC_images Raw Conversion

Histogram Type Constructor

List to XML Node Conversion

data_add_regions

Add Region to IFC_data Object

RIF/CIF Image Field Directories Extraction

getImagesValues

RIF/CIF Image Values Extraction

IFC Files Generic Reader

inv_smoothLinLog

Inverse Smooth LinLog Transformation

Lattice Key Panel Contructor

Histogram Constructor

Histogram Smooth Constructor

IFC_offset Subsetting

LinLog Transformation for IFC Graphs Plotting Scales

File Extenstion Removal

String Decomposition with Placeholders

Progress Bar Initializer

Object File Export

popsGetObjectsIds

IFC_pops Object Numbers

objectTransform

Object Transformation

popsGetSiblings

IFC_pops Sibling Population Identification

toXML2_features

IFC_features XML Conversion

IFC_pops Levels Dependency Determination

Ellipsoid Polygon Constructor

popsGetSiblings1

IFC_pops Sibling Population from Same Base Identification

Progress Bar Updater

LinLog Transformation of Ticks and Labels

IFC_images XML Conversion

IFC_masks XML Conversion

Input Identification

Histogram Val Constructor