Visualization of highly multiplexed imaging data in R


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Documentation for package ‘cytomapper’ version 1.20.0

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