Man pages for Nanostring-Biostats/SpatialOmicsOverlay
Spatial Overlay for Omic Data from Nanostring GeoMx Data
| add4ChannelImage | Add 4-channel image to SpatialOverlay from OME-TIFF. Allows... |
| addImageFile | Add image to SpatialOverlay from disk |
| addImageOmeTiff | Add image to SpatialOverlay from OME-TIFF |
| addPlottingFactor | Add plotting factor to 'SpatialOverlay' object |
| annotMatching | Match ROIs in annotation file to xml |
| bookendStr | Print long string in more managable fashion |
| changeColoringIntensity | Update color intensities for changing to RGB image |
| changeImageColoring | Update color scheme for changing to RGB image |
| checkValidRes | Determine lowest resolution image in OME-TIFF |
| createCoordFile | Create coordinate file for entire scan |
| createMask | Create a binary mask from a base 64 string |
| cropSamples | Crop to zoom in on given ROIs |
| cropTissue | Crop to remove black boundary around tissue. |
| downloadMouseBrainImage | Download Mouse Brain OME-TIFF from NanoString's Spatial Organ... |
| flipX | Flip x axis in image and overlay points |
| flipY | Flip y axis in image and overlay points |
| fluorLegend | Add legend of fluorescence targets that make up image |
| moveCoords | Move coordinates if they don't match image |
| parseOverlayAttrs | Parse the xml file for AOI attributes in GeoMx images |
| parseScanMetadata | Parse the xml file for the scan metadata of GeoMx images |
| plotSpatialOverlay | overlay plots |
| readLabWorksheet | Read lab worksheet into dataframe of annotations |
| readSpatialOverlay | Read in 'SpatialOverlay' from tiff file and annotations |
| recolor | recolor images after changing colors and/or color intensities |
| removeSample | Remove sample(s) from SpatialOverlay |
| SpatialOverlay-class | Class to Contain NanoString Spatial Overlay Images and Data |
| SpatialPosition-class | Class to Contain NanoString Spatial Overlay ROI information |
| xmlExtraction | Extract xml from OME-TIFF |
