Formatting the Visium data

library(Seurat)

Loading required package: SeuratObject

Loading required package: sp


Attaching package: ‘SeuratObject’


The following objects are masked from ‘package:base’:

    intersect, t

RAW_DATA_PATH <- "/import/home/share/zw/data/mouse_brain/visium"

# 10x Visium Slice 1
visium_data <- readRDS(file.path(RAW_DATA_PATH, "visium_1", "brain_visium_1.rds"))
counts <- visium_data@assays$RNA@counts
counts <- t(as.matrix(counts))
write.csv(counts, file = file.path(RAW_DATA_PATH, "visium_1", "mouse_brain_visium_1_counts.csv"))
coordinates <-  Embeddings(visium_data, reduction = "spatial")
write.csv(coordinates, file = file.path(RAW_DATA_PATH, "visium_1", "mouse_brain_visium_1_coordinates.csv"))

Warning message in asMethod(object):
“sparse->dense coercion: allocating vector of size 1.0 GiB”

# 10x Visium Slice 2
visium_data <- readRDS(file.path(RAW_DATA_PATH, "visium_2", "brain_visium_2.rds"))
counts <- visium_data@assays$RNA@counts
counts <- t(as.matrix(counts))
write.csv(counts, file = file.path(RAW_DATA_PATH, "visium_2", "mouse_brain_visium_2_counts.csv"))
coordinates <-  Embeddings(visium_data, reduction = "spatial")
write.csv(coordinates, file = file.path(RAW_DATA_PATH, "visium_2", "mouse_brain_visium_2_coordinates.csv"))