Fix R-CMD-Check failure (due to external data)

data-raw/merfish_mousePOA.R

@@ -16,6 +16,9 @@ bregma <- "-0.29"
 data_sub <- data[(data$Animal_ID == animal & data$Animal_sex == sex & data$Behavior == behavior & data$Bregma == bregma),]
 dim(data_sub)
 
+## save subsetted data for vignettes
+saveRDS(data_sub, file = here("vignettes/merfish_mousePOA_raw.RDS"))
+
 ## genes-by-cells matrix
 # extract the genes-by-cells matrix as a sparse matrix (dgCMatrix)
 mat <- as(t(data_sub[,10:ncol(data_sub)]), "CsparseMatrix")

vignettes/formatting-SpatialExperiment-for-SEraster.Rmd

@@ -19,7 +19,7 @@ knitr::opts_chunk$set(
 
 For this tutorial, we will format a preprocessed MERFISH dataset of the mouse preotic area (POA) into a `SpatialExperiment` so that it can be rasterized with `SEraster`. The output of this tutorial is the same as the `merfish_mousePOA` dataset in the package.
 
-In the original work, [Moffitt J. and Bambah-Mukku D. et al. (2018), "Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region", *Science Advances*](https://www.science.org/doi/10.1126/science.aau5324), authors collected spatial transcriptomics datasets of mouse POA regions for various sexes, behavioral conditions, and bregma sections. The full dataset can be downloaded from [Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.8t8s248). We only use the dataset for a bregma -0.29 slice from a female naive animal (Animal ID = 1).
+In the original work, [Moffitt J. and Bambah-Mukku D. et al. (2018), "Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region", *Science Advances*](https://www.science.org/doi/10.1126/science.aau5324), authors collected spatial transcriptomics datasets of mouse POA regions for various sexes, behavioral conditions, and bregma sections. The full dataset can be downloaded from [Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.8t8s248). We only use the dataset for a bregma -0.29 slice from a female naive animal (Animal ID = 1, Animal Sex = "Female", Behavior = "Naive", Bregma = "-0.29").
 
 ## Load libraries
 
@@ -29,20 +29,10 @@ library(Matrix)
 library(ggplot2)
 ```
 
-## Load dataset
+## Load the subsetted dataset
 
 ```{r}
-data <- read.csv('/Users/gohtaaihara/Downloads/Moffitt_and_Bambah-Mukku_et_al_merfish_all_cells.csv')
-```
-
-Subset the dataset to specific female, behavioral condition, and bregma section.
-
-```{r}
-animal <- 1
-sex <- "Female"
-behavior <- "Naive"
-bregma <- "-0.29"
-data_sub <- data[(data$Animal_ID == animal & data$Animal_sex == sex & data$Behavior == behavior & data$Bregma == bregma),]
+data_sub <- readRDS(file = here("vignettes/merfish_mousePOA_raw.RDS"))
 dim(data_sub)
 ```