## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----message=FALSE------------------------------------------------------------ library(SpatialExperiment) library(STexampleData) library(ggspavis) ## ----message=FALSE------------------------------------------------------------ # load data in SpatialExperiment format spe <- Visium_mouseCoronal() ## ----message=FALSE, out.width="60%"------------------------------------------- # add some values in 'colData' to annotate spots colData(spe)$sum <- colSums(counts(spe)) # example plots plotSpots(spe, annotate = "sum") plotVisium(spe, fill = "sum", trans = "log", highlight = "in_tissue") ## ----message=FALSE------------------------------------------------------------ # load data in SpatialExperiment format spe <- Visium_humanDLPFC() ## ----message=FALSE, out.width="60%"------------------------------------------- # example plots plotSpots(spe, annotate = "ground_truth", palette = "libd_layer_colors") plotVisium(spe, fill = "ground_truth", highlight = "in_tissue") ## ----message=FALSE------------------------------------------------------------ # load data in SpatialExperiment format spe <- seqFISH_mouseEmbryo() ## ----message=FALSE, out.width="60%"------------------------------------------- # example plots plotMolecules(spe, molecule = "Sox2") ## ----------------------------------------------------------------------------- sessionInfo()