markers_plots_files: Make plots of top markers.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Make plots of top markers.

Description

Make plots of top markers.

Usage

markers_plots_files(
  sce_dimred,
  markers_plots_top,
  save = TRUE,
  dry = FALSE,
  return_type = c("file", "plot", "tibble")
)

Arguments

sce_dimred	A SingleCellExperiment object with computed dimreds.
markers_plots_top	A tibble, output from markers_plots_top(). See cluster_markers_plots_top or contrasts_plots_top target for details.
save	A logical scalar: if TRUE, save each plot to markers_top$out_file.
dry	A logical scalar: if TRUE, do not make plots and just create empty files.
return_type	A character scalar: "file": return markers_top$out_file. "plot": return list of marker plots. "tibble": return a modified markers_plots_top tibble with appended marker_plot column (list of marker plots).

Value

See the return_type argument. See cluster_markers_plots_files or contrasts_plots_files target for details.

See Also

marker_plot()

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.