WHAT: one small UMAP per marker, coloured by that marker's asinh intensity. WHY: this is the check that the embedding is biologically structured – each lineage marker should light up a coherent region. If markers are smeared uniformly, the embedding is driven by noise (which is exactly what the ungated template produced).
Usage
fig_marker_grid(
cells,
markers,
outfile,
panel_label = "",
ncol = NULL,
dpi = 300,
panel_size = 2.5,
colors = fcs_colors(),
scale_label = "asinh intensity"
)Arguments
- cells
data.frame with umap_1/umap_2 plus one column per marker.
- markers
character vector of marker column names to render.
- outfile
Path to write the figure to.
- panel_label
Marker-panel name added to the figure title; empty for none. Default
"".- ncol
Number of panel columns; NULL computes one that keeps the canvas roughly square.
- dpi
Resolution in dots per inch. May be reduced automatically to respect the raster ceiling; see
safe_ggsave(). Default300.- panel_size
The panel size. Default
2.5.- colors
Named list of colours; defaults to the package palette. See
fcs_colors(). Defaultfcs_colors().- scale_label
Name of the scale the intensities are on, the run's
transform$label("asinh intensity", "logicle intensity"). Default"asinh intensity".