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Spatial Elemental Mapping

Source: vignettes/spatial-mapping.Rmd
spatial-mapping.Rmd

R-CMD-check pkgdown CRAN status Codecov test coverage CRAN downloads CRAN downloads total License: MIT Lifecycle: experimental

Raster scan dataset 

ds <- ls_example_data("spatial")
ds

The simulated tissue section has:

  • A left-to-right Ca gradient (decreasing)
  • A top-to-bottom Fe gradient (increasing)
  • A Zn-enriched hotspot simulating a tumor region

Build a single elemental map 

m_ca <- ls_build_map(ds, "Ca", 393.37)
ls_plot_map(m_ca)

Multi-element panel 

maps <- ls_map_elements(ds, c("Ca", "Fe", "Zn"),
                        c(Ca = 393.37, Fe = 371.99, Zn = 213.86))
ls_plot_map_panel(maps)

Applying a calibration to the map 

cal_ds <- ls_example_data("calibration")
cal <- ls_calibrate(cal_ds, "Ca", 393.37,
                    concentrations = cal_ds$sample_info$concentration,
                    verbose = FALSE)
m_cal <- ls_build_map(ds, "Ca", 393.37, calibration = cal)
ls_plot_map(m_cal)

Hotspot detection 

zn <- ls_build_map(ds, "Zn", 213.86)
hot_idx <- which(zn$values > stats::quantile(zn$values, 0.9))
head(data.frame(x = zn$x[hot_idx],
                y = zn$y[hot_idx],
                zn = round(zn$values[hot_idx], 1)))
#>    x y   zn
#> 1  8 3  9.5
#> 2  8 4  9.9
#> 3 10 4  9.1
#> 4  6 5 10.7
#> 5  9 5 11.3
#> 6  5 6  9.8