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Details Information: https://stack.xieguigang.me/2021/ggplot-msimaging-rsharp-scripting/
MS-imaging rendering package for R# environment based on the mzkit library and ggplot api
Mass spectrometry imaging ( MSI) is a technique used in mass spectrometry to visualize the spatial distribution of molecules, as biomarkers, metabolites, peptides or proteins by their molecular masses. After collecting a mass spectrum at one spot, the sample is moved to reach another region, and so on, until the entire sample is scanned.
require(MSImaging);
require(mzkit);
require(ggplot);
options(memory.load = "max");
bitmap(file = `${@dir}/HR2MSI_mouse_urinary_bladder_S096.png`, size = [4000, 2500]) {
# load mzpack/imzML raw data file
# and config ggplot data source driver
# as MSImaging data reader
ggplot(open.mzpack(system.file("data/HR2MSI mouse urinary bladder S096 - Figure1.cdf", package = "MSImaging")),
mapping = aes(driver = MSImaging()),
padding = "padding: 200px 600px 200px 250px;"
)
# rendering of a single ion m/z
# default color palette is Jet color set
+ geom_msimaging(mz = 741.5, tolerance = "da:0.3")
# add ggplot charting elements
+ ggtitle("MSImaging of m/z 741.5")
+ labs(x = "Dimension(X)", y = "Dimension(Y)")
+ scale_x_continuous(labels = "F0")
+ scale_y_continuous(labels = "F0")
;
}
require(MSImaging);
require(mzkit);
require(ggplot);
options(memory.load = "max");
bitmap(file = `${@dir}/HR2MSI_mouse_urinary_bladder_S096_RGB.png`, size = [3300, 2000]) {
# load mzpack/imzML raw data file
# and config ggplot data source driver
# as MSImaging data reader
ggplot(open.mzpack(system.file("data/HR2MSI mouse urinary bladder S096 - Figure1.cdf", package = "MSImaging")),
mapping = aes(driver = MSImaging()),
padding = "padding: 200px 600px 200px 250px;"
)
# rendering of rgb channels ion m/z
+ geom_red(mz = 743.5468, tolerance = "da:0.3")
+ geom_green(mz = 798.5414, tolerance = "da:0.3")
+ geom_blue(mz = 741.5303, tolerance = "da:0.3")
# add ggplot charting elements
+ ggtitle("HR2MSI mouse urinary bladder S096 - Figure1")
+ labs(x = "Dimension(X)", y = "Dimension(Y)")
+ scale_x_continuous(labels = "F0")
+ scale_y_continuous(labels = "F0")
;
}
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