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IFC (version 0.1.6)

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 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

0.1.6

License

GPL-3

Maintainer

Yohann Demont

Last Published

August 22nd, 2022

Functions in IFC (0.1.6)

Graphical and Statistic Report Display

DAF File Writer

Graphical and Statistic Report Generation

Batch Generation of Graphical and Statistic Report

Batch File Writer

Gallery Display

CreateGraphReport

Graph Report Generation

FCS File Writer

FCS_merge_dataset

FCS Object Data Sets Merging

ExtractMasks_toMatrix

Shorcut for Batch Masks Extraction to Matrices/Arrays

ExtractImages_toMatrix

Shorcut for Batch Images Extraction to Matrices/Arrays

IFC Graph Adjustment

ExtractImages_toBase64

Shorcut for Batch Images Extraction to Base64

ExtractImages_toFile

Shorcut for Batch Images Extraction to Files

Image Scale Bar Incrustation

Image Text Incrustation

RIF/CIF File Conversion to TIFF

FCS File Reader

applyGatingStrategy

Apply Gating Strategy

FCS_merge_sample

FCS Object Samples Merging

Apply Transformation

ExportToGallery

DAF File Reader

RIF/CIF File Writer

FCS Object Converter

RIF/CIF File Checksum

base_axis_constr

Axis Constructor

Raw Images to Base64 Encoding

IFC Feature Coercion

IFC Graph Coercion

Tools for Imaging Flow Cytometry

Image Field Directory Builder

buildPopulation

IFC Population Coercion

IFC Region Coercion

Matrix HSV to RGB Conversion

cpp_base64_encode

Raw to Base64 Conversion

2D Binned Kernel Density Estimation

IFC Statistics Coercion

Integer to Hexadecimal Color Conversion

IFC Mask Coercion

Spatial Offsets Image Correction

cpp_as_nativeRaster

Image to Native Raster Conversion

Character Color Check and RGB Conversion

`IFC_data` Object Check

Input Parameters Assertive Tool

cpp_int32_to_uint32

Int32 to Uint32 32bits Conversion

Matrix Cropping

DAF File Checksum

IFC Files Checksum

Raw Vectors Collapse

RIF/CIF File Reader

Automatic Parameters Detection for IFC Graphs

Image Gamma Computation

Assert that Certain Conditions are Met

IFC_object Decompression

base_hist_constr

Histogram Constructor for 'base' Plot

cpp_computeGamma

Gamma Computation

cpp_int64_to_uint64

Int64 to Uint64 64bits Conversion

IFC File Information Extraction

IFC_object Extraction

IFD Fast Tags Extraction

cpp_fast_cbind_M_M

Matrix and Matrix Column Binding

cpp_fast_cbind_M_DF

Fast Matrix and Dataframe Column Binding

cpp_fast_cbind_DF_DF

Dataframe and Dataframe Column Binding

convert_spillover

Spillover Converter

User's Coordinates to Pixels Conversion

cpp_fast_factor

Fast Factorize Vector

cpp_fast_listAny

Use Rcpp to Apply Any on List members

cpp_inv_smoothLinLog

Inverse Smooth LinLog Transformation with Rcpp

Matrix to Matrix Writer According to Mask with Offsets

cpp_fast_cbind_DF_L

Fast Dataframe and List Column Binding

cpp_fast_cbind_L_DF

Fast List and Dataframe Column Binding

cpp_fast_cbind_DF_M

Fast Dataframe and Matrix Column Binding

cpp_uint32_to_int32

Uint32 to Int32 32bits Conversion

cpp_smoothLinLog

Smooth LinLog Transformation with Rcpp

cpp_v_int64_to_uint64

Vectorize Int64 to Uint64 64bits Conversion

Matrix Transformation

data_add_features

Add Feature to IFC_data Object

cpp_getoffsets_wid

IFC_offsets Computation with Object Identification

cpp_uint32_to_raw

Uint32 to Raw Conversion

cpp_replace_non_finite

Non Finite Values Replacement

Data Frame Merge Groups with Rcpp

Combine by Columns

cpp_fast_sample

Use Rcpp for Sampling

data_add_regions

Add Region to IFC_data Object

Add Population to IFC_data Object

cpp_coord_to_px

Coordinates to Pixels

IFC_object Decompression to RAW

Colors for Smooth Density Plots

IFD Tags Extraction

Progress Bar Terminator

fromXML2_gating

GatingML Conversion from XML2

File Path Placeholders Formatting

cpp_get_bytes_order

Get Bytes Order

cpp_getoffsets_noid

IFC_offsets Computation without Id Determination

RIF/CIF File Image Field Directories Offsets Extraction

Luminance Computation

cpp_pnt_in_gate

get_coordmap_adjusted

Device Adjusted Coordinates

RIF/CIF File Merging

cpp_uint64_to_int64

Uint64 to Int64 64bits Conversion

Image Gamma Modification

Populations Renaming

R/IDEAS Color Palette Mapping

Object File Export

Ellipse Boundaries to Coordinates

Checksum for RIF/CIF

Matrix Cleanser

Draw Shape to Image

cpp_v_int32_to_uint32

Vectorize Int32 to Uint32 32bits Conversion

popsRetrieveGraph

Graph Retrieval from Graphical IFC_pops

Name Protection

Random Name Generator

Histogram y-Axis Limits Constructor

get_coordmap_raw

Device Raw Coordinates

Feature Default Name Computation

objectTransform

Object Transformation

Object Resizing

ASSIST Database Extraction

Aborted Batch Files Retrieval

inv_smoothAsinh

Inverse Smooth Asinh Transformation

Object Cleanser

Hexadecimal to Integer Color Conversion

XML Node List Expansion

escape_entities

XML Entities Protection

redefine_features_def_feat

IFC_features_def Feature Redefinition

data_rm_regions

Remove Region from an IFC_data Object

data_add_pop_sample

Population Sampling

DAF File Writer

File Extension Retrieval

Smooth LinLog Transformation

redefine_features_def_msk_img

IFC_features_def Mask or Image Redefinition

Use Rcpp for Range

cpp_fast_rowAny

Use Rcpp to Apply Any on Matrix Rows

IFC_pops Computation

FCS File Parser

Copy Populations from One File to Another File

popsGetObjectsIds

IFC_pops Object Numbers

RIF/CIF Image Field Directories Extraction

popsGetSiblings

IFC_pops Sibling Population Identification

Groups Combination

getImagesValues

RIF/CIF Image Values Extraction

Object Colorizer

Image Field Directory Full Tag Retrieval

IFC_graphs XML Conversion

Lattice Key Panel Contructor

toXML2_graphpop_gs

Graphical Population GatingML Conversion to XML2

Special Character Replacement

FCS Name Parser

Histogram Smooth Constructor

Histogram Constructor

Lattice Histogram Panel Contructor

Image Field Directory Writer

objectNormalize

Object Intensity Normalization

Object Extraction Parameters Definition

Equal Sized Matrix to Matrix Writer According to Mask

Matrix Resizing

Statistics Extraction

data_rm_features

Remove Features from an IFC_data Object

Matrix Normalization

Remove Population from an IFC_data Object

Scale Constructor for IFC Graphs Plotting

List to XML Conversion

IFC_data Channel Swap

IFC_pops Checker for Object Membership to Populations

File Extension Removal

`IFC_plot` Conversion to 'raster' Plot

inv_smoothLinLog

Inverse Smooth LinLog Transformation

`IFC_plot` Statistics Extraction

Progress Bar Initializer

IFC_pops Network Display

IFC_pops Population Level Ordering

Next Component Prediction

Report Layout Extraction

String Truncation

List to XML Node Conversion

RIF/CIF Image Order Test

toXML2_features

IFC_features XML Conversion

toXML2_features_def

IFC_features_def XML Conversion

Text to Image Conversion

IFC_masks Redefinition

Numeric to String Formatting

IFC_regions XML Conversion

IFC_features Raw Conversion

IFC Files Generic Writer

writeGatingStrategy

Gating Strategy File Writer

toXML2_spillover_gs

Spillover GatingML Conversion

redefine_masks_image

IFC_masks Image Redefinition

`IFC_plot` Conversion to 'base' Plot

`IFC_plot` Conversion to 'lattice' Plot

popsGetAffiliation

IFC_pops Affiliation Finder

Object Extraction

Plot and Stats Computation for IFC Graph

readGatingStrategy

Gating Strategy File Reader

Parse Transformation Information

GatingML File Reader

IFC_pops Levels Dependency Determination

redefine_masks_mask

IFC_masks Mask Redefinition

IFC_data Redefinition

IFC_images Raw Conversion

IFC_masks XML Conversion

First Letter Only Capitalization

IFC_stats Computation

String Decomposition with Placeholders

File Path Decomposition

IFC Files Generic Reader

popsGetSiblings1

IFC_pops Sibling Population from Same Base Identification

popsGetSiblings2

IFC_pops Sibling Population from Same Region Identification

Boolean Expression Validation

IFC_pops XML Conversion

Smooth Asinh Transformation

IFC_offset Subsetting

Progress Bar Updater

redefine_features_def

IFC_features_def Redefinition

RIF/CIF File Subsetting

Input Identification

IFC_images XML Conversion

toXML2_graphs_gs

IFC_graphs GatingML Conversion

IFC_data Default Naming

toXML2_boolpop_gs

Boolean Population GatingML Conversion to XML2

String Decomposition with Operators

Ellipsoid Polygon Constructor

tryReportFileCreation

Report File Creation

IFC_stats XML Conversion

XML Node to List Conversion

Histogram Type Constructor

Histogram Val Constructor