spatGenePlot2D

Visualize cells and gene expression according to spatial coordinates

spatGenePlot2D(
  gobject,
  show_image = F,
  gimage = NULL,
  image_name = "image",
  sdimx = "sdimx",
  sdimy = "sdimy",
  expression_values = c("normalized", "scaled", "custom"),
  genes,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  show_network = F,
  network_color = NULL,
  spatial_network_name = "Delaunay_network",
  edge_alpha = NULL,
  show_grid = F,
  grid_color = NULL,
  spatial_grid_name = "spatial_grid",
  midpoint = 0,
  scale_alpha_with_expression = FALSE,
  point_shape = c("border", "no_border", "voronoi"),
  point_size = 1,
  point_alpha = 1,
  point_border_col = "black",
  point_border_stroke = 0.1,
  show_legend = T,
  legend_text = 8,
  background_color = "white",
  vor_border_color = "white",
  vor_alpha = 1,
  vor_max_radius = 200,
  axis_text = 8,
  axis_title = 8,
  cow_n_col = 2,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatGenePlot2D"
)

Arguments

gobject

giotto object

show_image

show a tissue background image

gimage

a giotto image

image_name

name of a giotto image

sdimx

x-axis dimension name (default = 'sdimx')

sdimy

y-axis dimension name (default = 'sdimy')

expression_values

gene expression values to use

genes

genes to show

cell_color_gradient

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

show_network

show underlying spatial network

network_color

color of spatial network

spatial_network_name

name of spatial network to use

edge_alpha

alpha of edge

show_grid

show spatial grid

grid_color

color of spatial grid

spatial_grid_name

name of spatial grid to use

midpoint

expression midpoint

scale_alpha_with_expression

scale expression with ggplot alpha parameter

point_shape

shape of points (border, no_border or voronoi)

point_size

size of point (cell)

point_alpha

transparancy of points

point_border_col

color of border around points

point_border_stroke

stroke size of border around points

show_legend

show legend

legend_text

size of legend text

background_color

color of plot background

vor_border_color

border colorr for voronoi plot

vor_alpha

transparancy of voronoi 'cells'

vor_max_radius

maximum radius for voronoi 'cells'

axis_text

size of axis text

axis_title

size of axis title

cow_n_col

cowplot param: how many columns

cow_rel_h

cowplot param: relative height

cow_rel_w

cowplot param: relative width

cow_align

cowplot param: how to align

show_plot

show plots

return_plot

return ggplot object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters, see showSaveParameters

default_save_name

default save name for saving, don't change, change save_name in save_param

Value

ggplot

Details

Description of parameters.

See also

spatGenePlot3D

Other spatial gene expression visualizations: spatGenePlot3D(), spatGenePlot()

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
spatGenePlot2D(mini_giotto_single_cell, genes = selected_genes, point_size = 3)