Plot wrapper function. — wrapper_for

A wrapper function for plots that are often used during exploratory analysis within the Seurat framework (https://satijalab.org/seurat/). Includes FeaturePlot, DimPlot for different parameters, and ratio_cluster_plot.

Usage

wrapper_for_plots(
  obj = obj,
  feature_plot = TRUE,
  cluster_plot = TRUE,
  meta_list = list("ratio_anno"),
  cluster_handle = "sketch_snn_res",
  feature_plot_colors = pals::parula(1000),
  ratio_plot_color = c(Ratio_low = "dodgerblue2", Ratio_high = "gold2"),
  reduction = "umap",
  alpha = 1,
  raster = F,
  label_size = 3,
  label_box = FALSE,
  assay = "sketch"
)

Arguments

obj: The Seurat object.
feature_plot: Boolean. TRUE indicates that UMAP is colored for all features (see FeaturePlot)
cluster_plot: Boolean. TRUE indicates that UMAP is colored by the different cluster resolutions stored with the cluster_handle.
meta_list: List of meta.data columns to color DimPlot by. Can be both numeric to generate FeaturePlot or class character or factor for DimPlot.
cluster_handle: Prefix for the clustering solutions in the meta.data slot.
feature_plot_colors: Color palette for FeaturePlot.
ratio_plot_color: Color palette for ratio_cluster_plot.
reduction: Reduction to use for plotting, for example UMAP.
alpha: Alpha value for plotting.
raster: Convert points to raster format. If TRUE plot is rasterized to raster.dpi=c(512, 512). Requires ggrastr.
label_size: Size of the labels plotted within the embedding.
label_box: Plot boxes around labels in the color of the cluster.
assay: The Seurat assay (default FACS).

Value

A list with the requested plots.