The function return a plot visualizing the immunofluoresence staining images associated with a list of FOVs provided by the user. When no list is provided, all FOVs represented in the input file will be plotted.
CosmxFovPlot(fovs = NULL, which = NULL, img_dir = NULL, maxres = 2000)data frame containing FOV geometries (square) created via the read_fovfile() function from Kandinsky
vector of FOV identifier to be considered for plotting
character stringr specifying the full path of the directory containing Cosmx FOV images (usually named "CellComposite", but other type of images can be selected, such as 'CellOverlay','CellLabels', or 'Morphology2D')
image resolution threshold. Will be applied to each image separately. When several images are selected for plotting, it is advisable to set a low maxres value (within the 500-800 range) to speed up the processing time
plot of concatenated FOV images
This function is designed to work with CosMx data only.