WHAT: writes the main UMAP figure (population identity, sample, and any patient covariates present) for one panel group. WHY: one shared embedding viewed many ways is what makes populations comparable across patients; separate embeddings per sample would give coordinates that cannot be compared.
Usage
fig_umap_overview(
cells,
outfile,
panel_label = "",
covariates = NULL,
feature_cols = character(0),
width = 15,
height = 11,
dpi = 300,
colors = fcs_colors()
)Arguments
- cells
data.frame with umap_1, umap_2, population_label, sample_id and optionally covariate columns.
- outfile
Path to write the figure to.
- panel_label
Marker-panel name added to the figure title; empty for none. Default
"".- covariates
NULL (default) to DISCOVER plottable covariates from the joined table, or an explicit character vector to fix the set.
WHY discovery is the default: a fixed list can only plot the covariates someone anticipated. The single most important variable in a case-control study is the group column – cohort, genotype, treatment arm – and its name is study-specific, so a hardcoded list silently omits exactly the panel the experiment was designed to produce. Anything that arrives from the sample map or patient table and varies across cells is plottable; the exclusion list below is structural (coordinates, gate bookkeeping, marker intensities), because those are plotted by other figures or are not covariates at all.
- feature_cols
The feature cols. Default
character(0).- width
Figure width in inches. Default
15.- height
Figure height in inches. Default
11.- dpi
Resolution in dots per inch. May be reduced automatically to respect the raster ceiling; see
safe_ggsave(). Default300.- colors
Named list of colours; defaults to the package palette. See
fcs_colors(). Defaultfcs_colors().