# Visualization of highly multiplexed imaging data in R

## Documentation for package ‘cytomapper’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

channelNames | Getting and setting the channel and image names
channelNames-method | Getting and setting the channel and image names
channelNames<- | Getting and setting the channel and image names
channelNames<--method | Getting and setting the channel and image names
coerce-method | S4 class for list of images
compImage | Performs channel compensation on multi-channel images
CytoImageList | S4 class for list of images
CytoImageList-class | S4 class for list of images
CytoImageList-manipulation | Manipulating CytoImageList objects
CytoImageList-naming | Getting and setting the channel and image names
CytoImageList-subsetting | General subsetting methods for CytoImageList objects
cytomapperShiny | Shiny application to visualise gated cells on images
getChannels | General subsetting methods for CytoImageList objects
getChannels-method | General subsetting methods for CytoImageList objects
getImages | General subsetting methods for CytoImageList objects
getImages-method | General subsetting methods for CytoImageList objects
loadImages | Read images into CytoImageList object
measureObjects | Compute morphological and intensity features from objects on images.
mergeChannels | General subsetting methods for CytoImageList objects
names-method | Getting and setting the channel and image names
names<--method | Getting and setting the channel and image names
normalize | Manipulating CytoImageList objects
normalize-method | Manipulating CytoImageList objects
pancreasImages | Example CytoImageList object of image files
pancreasMasks | Example CytoImageList object of segmentation masks
pancreasSCE | Example SingleCellExperiment object
plotCells | Function to visualize cell-level information on segmentation masks
plotPixels | Function to visualize pixel-level information of multi-channel images
plotting-param | Further plotting parameters for the cytomapper package
scaleImages | Manipulating CytoImageList objects
scaleImages-method | Manipulating CytoImageList objects
setChannels<- | General subsetting methods for CytoImageList objects
setChannels<--method | General subsetting methods for CytoImageList objects
setImages<- | General subsetting methods for CytoImageList objects
setImages<--method | General subsetting methods for CytoImageList objects
show-method | S4 class for list of images
[<--method | General subsetting methods for CytoImageList objects
[[<--method | General subsetting methods for CytoImageList objects