MsImaging


        require(mzkit);
                               

#' Visual MS imaging data(*.imzML)
imports "MsImaging" from "mzplot";

Visual MS imaging data(*.imzML)

Mass spec imaging (MSI) is a technique measuring chemical composition and linking it to spatial coordinates on a surface. The chemical composition is determined by mass spectrometry, which measures the mass-to-charge ratios (m/z's) of any ions that can be generated from the surface. Most commonly, the surface is a tissue section on a microscope slide; however, any flat surface could be analyzed given it has suitable dimensions and is properly prepared.

.NET clr function exports
as.data.frame.singleionlayer	SingleIonLayer: a collection of the PixelData spots, the spot pixel data was used to the spatial heatmap rendering.
split.layer	split the ms-imaging layer into multiple parts
TrIQ	Contrast optimization of mass spectrometry imaging(MSI) data visualization by threshold intensity quantization (TrIQ)
intensityLimits	trim the intensity data value in a pixels of a ion MS-Imaging layer
apply_raster_filter	apply a single filter or a filter pipeline
write.mzImage	write mzImage data file
read.mzImage	open the existed mzImage cache file
FilterMz	Extract a spectrum matrix object from MSI data by a given set of m/z values
MS1	get the ms1 spectrum data in a specific pixel position
viewer	load imzML data into the ms-imaging render
pixel	get the spatial spot pixel data
ionLayers	load the raw pixels data from imzML file
tag_layers	set cluster tags to the pixel tag property data
sum_layers	merge multiple layers via intensity sum
rgb	rendering ions MSI in (R,G,B) color channels
MSIlayer	get MSI pixels layer via given `m/z` value.
intensity	Get intensity data vector from a given MS-imaging layer
knnFill	do pixel interpolation for run MS-imaging
MSI_coverage
assert	test of a given MSI layer is target?
layer	render a ms-imaging layer by a specific `m/z` scan.
MSI_summary.scaleMax	Get the max intensity value via TrIQ or quantile cutoff
defaultFilter	get the default ms-imaging filter pipeline
parseFilters	Converts R raw vector input into a raster processing pipeline configuration
intensityFilter
render	MS-imaging of the MSI summary data result.
as.pixels	extract the pixel [x,y] information for all of the points in the target `layer`
MeasureMSIions