nice_spatial_feature_plot: nice_spatial_feature_plot

In mvhunter1/mvhspatialplots: Some improved functions for analysis of ST and GSEA data.

Description

nicer looking version of the Seurat function SpatialFeaturePlot.

Usage

nice_spatial_feature_plot(
  seurat_obj,
  features,
  im_alpha = 0,
  pt_size = 1.4,
  stroke = 0,
  new_cmap = T,
  cmap = "inferno",
  n_col = NULL,
  diverging_cmap = T,
  alpha = T,
  cols = NULL
)

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.
pt.size	size of plotted points.

Value

SpatialFeaturePlot.

mvhunter1/mvhspatialplots documentation built on April 24, 2021, 10:52 a.m.