spatGenePlot2Dsce: A function for visualization selected genes in pseudotissue...

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

A function for visualization selected genes in pseudotissue visualization

Description

Adapted function from Giotto package Dries et al, 2021, rewrite for use in scdrake package for a SingleCellExperiment object

Usage

spatGenePlot2Dsce(
  sce,
  sdimx = "Dims_x",
  sdimy = "Dims_y",
  expression_values = c("counts", "logcounts"),
  genes,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  edge_alpha = NULL,
  scale_alpha_with_expression = FALSE,
  point_shape = c("border", "no_border"),
  point_size = 1,
  point_alpha = 1,
  point_border_col = "black",
  point_border_stroke = 0.1,
  show_legend = T,
  legend_text = 8,
  background_color = "white",
  axis_text = 8,
  axis_title = 8,
  cow_n_col = 2,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h"
)

Arguments

sce	A SingleCellExperiment object.

Value

A ggplot2 object.

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