nice_spatial_feature_plot: nice_spatial_feature_plot

In mvhunter1/mvhfunctions:

nice_spatial_feature_plot

Description

nicer looking version of the Seurat function SpatialFeaturePlot.

Usage

nice_spatial_feature_plot(
  seurat_obj,
  features,
  im_alpha = 0,
  pt_size = 1.3,
  stroke = 0,
  new_cmap = T,
  cmap = "inferno",
  n_col = 3,
  diverging_cmap = F,
  alpha = T,
  cols = NULL,
  crop = T,
  min.cutoff = 0,
  max.cutoff = NA
)

Arguments

seurat_obj	Seurat object.
features	genes to plot.
im_alpha	set to 1 to plot the tissue image, 0 otherwise.
stroke	linewidth to outline plotted points in black (default = no outline).
new_cmap	if T, change the colourmap from Seurat default.
cmap	colourmap to use if new_cmap = T.
n_col	if plotting multiple genes, number of columns in final plot_grid object.
diverging_cmap	if T, will fill points with diverging colours between blue and red. otherwise, will use a linear colourmap.
alpha	if T, will fill points such that lower expression values are more transparent.
cols	optional: gradient vector of colours to use for plotting.
crop	Crop tissue array to focus on region with spots?
min.cutoff	Minimum value to bin expression data within
max.cutoff	Max value to bin expression data within
pt.size	size of plotted points.

Value

SpatialFeaturePlot.

mvhunter1/mvhfunctions documentation built on May 31, 2024, 3:36 p.m.