matrices.R
In h5lite: Simplified 'HDF5' Interface

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----setup--------------------------------------------------------------------
library(h5lite)
file <- tempfile(fileext = ".h5")

## -----------------------------------------------------------------------------
# Create a 3x4 matrix
mat <- matrix(1:12, nrow = 3, ncol = 4)

# Write to file
h5_write(mat, file, "linear_algebra/mat_a")

# Read back
mat_in <- h5_read(file, "linear_algebra/mat_a")

# Verify
all.equal(mat, mat_in)

## -----------------------------------------------------------------------------
# Create a 3D array (e.g., spatial data over time: x, y, time)
vol <- array(runif(24), dim = c(4, 3, 2))

h5_write(vol, file, "spatial/volume")

# Check dimensions without reading the full data
h5_dim(file, "spatial/volume")

## -----------------------------------------------------------------------------
# Create a matrix with row and column names
data <- matrix(rnorm(6), nrow = 2)
rownames(data) <- c("Sample_A", "Sample_B")
colnames(data) <- c("Gene_1", "Gene_2", "Gene_3")

h5_write(data, file, "genetics/expression")

# Read back
data_in <- h5_read(file, "genetics/expression")

print(data_in)

## -----------------------------------------------------------------------------
# Large matrix of zeros (highly compressible)
sparse_mat <- matrix(0, nrow = 1000, ncol = 1000)
sparse_mat[1:10, 1:10] <- 1

# Write with default compression (zlib level 5)
h5_write(sparse_mat, file, "compressed/matrix")

# Write with high compression (zlib level 9)
h5_write(sparse_mat, file, "compressed/matrix_max", compress = "gzip-9")

## ----include=FALSE------------------------------------------------------------
unlink(file)