## ----style, echo=FALSE-------------------------------------------------------- knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE, fig.retina = 0.75) library(BiocStyle) ## ----library, echo=FALSE, results='hide'-------------------------------------- suppressPackageStartupMessages(c( library(SingleCellExperiment), library(cytomapper), library(imcdatasets) )) ## ----list-datasets------------------------------------------------------------ datasets <- listDatasets() datasets <- as.data.frame(datasets) datasets$FunctionCall <- sprintf("`%s`", datasets$FunctionCall) knitr::kable(datasets) ## ----import-dataset----------------------------------------------------------- sce <- IMMUcan_2022_CancerExample("sce") sce ## ----import-images------------------------------------------------------------ images <- IMMUcan_2022_CancerExample("images") images ## ----import-masks------------------------------------------------------------- masks <- IMMUcan_2022_CancerExample("masks") masks ## ----on_disk------------------------------------------------------------------ # Create temporary location cur_path <- tempdir() masks <- IMMUcan_2022_CancerExample(data_type = "masks", on_disk = TRUE, h5FilesPath = cur_path) masks ## ----function-help------------------------------------------------------------ ?IMMUcan_2022_CancerExample ## ----access-metadata, eval = FALSE-------------------------------------------- # IMMUcan_2022_CancerExample(data_type = "sce", metadata = TRUE) # IMMUcan_2022_CancerExample(data_type = "images", metadata = TRUE) # IMMUcan_2022_CancerExample(data_type = "masks", metadata = TRUE) ## ----usage-subset------------------------------------------------------------- cur_images <- images[1:5] cur_masks <- masks[1:5] ## ----usage-pixel-------------------------------------------------------------- plotPixels( cur_images, colour_by = c("CD8a", "CD68", "CDH1"), bcg = list( CD8a = c(0,4,1), CD68 = c(0,5,1), CDH1 = c(0,5,1) ) ) ## ----usage-cell--------------------------------------------------------------- plotCells( cur_masks, object = sce, img_id = "image_number", cell_id = "cell_number", colour_by = c("CD8a", "CD68", "CDH1"), exprs_values = "exprs" ) ## ----usage-outline------------------------------------------------------------ plotPixels( cur_images, mask = cur_masks, object = sce, img_id = "image_number", cell_id = "cell_number", outline_by = "cell_type", colour_by = c("CD8a", "CD68", "CDH1"), bcg = list( CD8a = c(0,5,1), CD68 = c(0,5,1), CDH1 = c(0,5,1) ) ) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()