Spatial intensity plot for a QPTIFFImage or SpatialExperiment

For a QPTIFFImage: renders up to 10 channels as an additive colour composite on a black background. Each channel is assigned a distinct colour; its per-pixel intensity (min-max normalised to [0, 1]) drives the channel's contribution - high-intensity pixels appear fully saturated while low-intensity pixels are transparent (black). Channels that overlap in space produce mixed additive colours (e.g. cyan + red -> white), matching the standard composite view in FIJI / napari. When no markers are provided the first 10 channels (by index) are displayed.

Usage

plot_qptiff(
  x,
  markers = NULL,
  resolution = 1L,
  palette = "magma",
  assay.type = "bgnorm",
  scale = c("marker", "sample", "none"),
  point_size = 1,
  pixels = c(1024L, 1024L),
  flip_y = TRUE,
  large_data_threshold = 10000L,
  ncol = NULL
)

Arguments

x

A QPTIFFImage or a SpatialExperiment.

markers

Character vector of channel names to display, or NULL to use the first 10 channels (for QPTIFFImage) or all features (for SpatialExperiment). At most 10 channels are shown for QPTIFFImage input; excess channels are dropped with a warning.

resolution

Positive integer; pixel downsample factor for QPTIFFImage input (ignored for SpatialExperiment).

palette

Viridis palette name used for SpatialExperiment input only. Default "magma".

assay.type

Assay to visualise when x is a SpatialExperiment. Default "bgnorm".

scale

Character; intensity scaling for QPTIFFImage input (ignored for SpatialExperiment). One of:

"marker": (default) Per-channel min and 99.9th-percentile; each marker is stretched to full brightness independently.
"sample": Global min and 99.9th-percentile computed across all channels in the image; preserves relative intensities between markers.
"none": No scaling; values are clamped to [0, 1].

point_size

Base point size for SpatialExperiment scatter.

pixels

Integer c(width, height) for scattermore rasterisation. Default c(1024L, 1024L).

flip_y

Logical; reverse y-axis for SpatialExperiment? Default TRUE.

large_data_threshold

Cell count above which scattermore is used automatically. Default 10000L.

ncol

Ignored for QPTIFFImage (single composite panel). Number of facet columns for SpatialExperiment.

Value

A ggplot object.

Details

For a SpatialExperiment: plots each cell at its spatial coordinates, coloured by its (per-channel scaled) intensity from the requested assay using a viridis colour scale and dark theme. When the cell count exceeds large_data_threshold and scattermore is installed, the scatter layer is rasterised automatically.

Examples

path <- system.file("extdata", "PA_HNC_sample.ome.tiff", package = "bgnormR")
img  <- read_qptiff(path)
#> Reading TIFF directory structure ...
#> Reading OME-TIFF metadata ...
#> Reading IFD page layouts ...
#> Loading 5 channel(s) ...
#> Loading 5 channel(s) ...
plot_qptiff(img, markers = c("PanCK", "CD20"))


# \donttest{
# After normalisation: plot background-adjusted intensities
res <- bgnorm_pixels(img, sample_prop = 0.1)
plot_qptiff(res, markers = c("PanCK", "CD20"), scale = "sample")

# }