write_svg: Exporting each spatial heatmap to a separate SVG file

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Exporting each spatial heatmap to a separate SVG file

Description

This function exports each spatial heatmap (associated with a specific gene and condition) as separate SVG files. In contrast to the original aSVG file, spatial features in the output SVG files are assigned heat colors.

Usage

write_svg(input, out.dir)

Arguments

input	The output returned by shm or covis.
out.dir	The directory path where the colored aSVG file will be saved.

Value

Nothing is returned.

Author(s)

Jianhai Zhang [e-mail]
Dr. Thomas Girke [e-mail]

References

Hadley Wickham, Jim Hester and Jeroen Ooms (2019). xml2: Parse XML. R package version 1.2.2. https://CRAN.R-project.org/package=xml2

Examples

# Read the aSVG file.
svg.hum.pa <- system.file("extdata/shinyApp/data", 'homo_sapiens.brain.svg', 
package="spatialHeatmap")
svg.hum <- read_svg(svg.hum.pa)
# Attributes of spatial features.
feature.hum <- attribute(svg.hum)[[1]]
set.seed(20) # To obtain reproducible results, a fixed seed is set.
# Spatial features.
unique(feature.hum$feature)[1:10]
# Create a random numeric vector.
my_vec <- setNames(sample(1:100, 4), c('substantia.nigra', 'putamen', 
'prefrontal.cortex', 'notMapped'))
my_vec
# Plot spatial heatmaps with the imported aSVG and random vector.
dat.quick <- SPHM(svg=svg.hum, bulk=my_vec)
shm.res <- shm(data=dat.quick, ID='testing', ncol=1, sub.title.size=20, legend.nrow=3,
bar.width=0.1)
# Export each spatial heatmap (under a certain gene and condition) to a separate SVG 
# file in a temporary directory.
write_svg(input=shm.res, out.dir=tempdir(check = TRUE))

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.