Visualization of highly multiplexed imaging data in R
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Documentation for package ‘cytomapper’ version 1.21.0
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 |