I'm trying to load the gene count sparse matrix from this source in R:
However the matrix's contents appear to be empty. To download I used wget on the command line:
wget -O - https://shendure-web.gs.washington.edu/content/members/cao1025/public/mouse_embryo_atlas/gene_count.txt | head > data.txt
And then load matrix like so:
matrix <- Matrix::readMM(file="~/scratch/rtrujillo/RNA-seq/sci-seq/data.txt")
To ensure these two steps are successful I attempted to graph the counts per cell:
counts_per_cell <- Matrix::colSums(matrix)
plot <- ggplot() + aes(counts_per_cell)+ geom_histogram(binwidth=0.5, colour="black", fill="white") ggsave(plot,file="counts_per_cell.png")
Which returns this plot.
My interpretation is that there are zero counts for all 2 millions of the cells. Am I performing any of these steps incorrectly or is the matrix really completely empty?