spatDimGenePlot2D: spatDimGenePlot2D
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

spatDimGenePlot2D

R Documentation

spatDimGenePlot2D

Description

Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode

Usage

spatDimGenePlot2D(
  gobject,
  show_image = F,
  gimage = NULL,
  image_name = "image",
  expression_values = c("normalized", "scaled", "custom"),
  plot_alignment = c("vertical", "horizontal"),
  genes,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  dim_point_shape = c("border", "no_border"),
  dim_point_size = 1,
  dim_point_alpha = 1,
  dim_point_border_col = "black",
  dim_point_border_stroke = 0.1,
  show_NN_network = F,
  show_spatial_network = F,
  dim_network_color = "gray",
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  dim_edge_alpha = NULL,
  scale_alpha_with_expression = FALSE,
  sdimx = "sdimx",
  sdimy = "sdimy",
  spatial_network_name = "Delaunay_network",
  spatial_network_color = NULL,
  show_spatial_grid = F,
  grid_color = NULL,
  spatial_grid_name = "spatial_grid",
  spat_point_shape = c("border", "no_border", "voronoi"),
  spat_point_size = 1,
  spat_point_alpha = 1,
  spat_point_border_col = "black",
  spat_point_border_stroke = 0.1,
  spat_edge_alpha = NULL,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  cow_n_col = 2,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_legend = T,
  legend_text = 8,
  dim_background_color = "white",
  spat_background_color = "white",
  vor_border_color = "white",
  vor_max_radius = 200,
  vor_alpha = 1,
  axis_text = 8,
  axis_title = 8,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatDimGenePlot2D"
)

Arguments

`gobject`	giotto object
`show_image`	show a tissue background image
`gimage`	a giotto image
`image_name`	name of a giotto image
`expression_values`	gene expression values to use
`plot_alignment`	direction to align plot
`genes`	genes to show
`dim_reduction_to_use`	dimension reduction to use
`dim_reduction_name`	dimension reduction name
`dim1_to_use`	dimension to use on x-axis
`dim2_to_use`	dimension to use on y-axis
`dim_point_shape`	dim reduction points with border or not (border or no_border)
`dim_point_size`	dim reduction plot: point size
`dim_point_alpha`	transparancy of dim. reduction points
`dim_point_border_col`	color of border around points
`dim_point_border_stroke`	stroke size of border around points
`show_NN_network`	show underlying NN network
`show_spatial_network`	show underlying spatial netwok
`dim_network_color`	color of NN network
`nn_network_to_use`	type of NN network to use (kNN vs sNN)
`network_name`	name of NN network to use, if show_NN_network = TRUE
`dim_edge_alpha`	dim reduction plot: column to use for alpha of the edges
`scale_alpha_with_expression`	scale expression with ggplot alpha parameter
`sdimx`	spatial x-axis dimension name (default = 'sdimx')
`sdimy`	spatial y-axis dimension name (default = 'sdimy')
`spatial_network_name`	name of spatial network to use
`spatial_network_color`	color of spatial network
`show_spatial_grid`	show spatial grid
`grid_color`	color of spatial grid
`spatial_grid_name`	name of spatial grid to use
`spat_point_shape`	spatial points with border or not (border or no_border)
`spat_point_size`	spatial plot: point size
`spat_point_alpha`	transparancy of spatial points
`spat_point_border_col`	color of border around points
`spat_point_border_stroke`	stroke size of border around points
`spat_edge_alpha`	edge alpha
`cell_color_gradient`	vector with 3 colors for numeric data
`gradient_midpoint`	midpoint for color gradient
`gradient_limits`	vector with lower and upper limits
`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_legend`	show legend
`legend_text`	size of legend text
`dim_background_color`	color of plot background for dimension plot
`spat_background_color`	color of plot background for spatial plot
`vor_border_color`	border colorr for voronoi plot
`vor_max_radius`	maximum radius for voronoi 'cells'
`vor_alpha`	transparancy of voronoi 'cells'
`axis_text`	size of axis text
`axis_title`	size of axis title
`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

Details

Description of parameters.

Value

ggplot

Examples


data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1]
spatDimGenePlot2D(mini_giotto_single_cell, genes = selected_genes,
                 dim_point_size = 3, spat_point_size = 3,
                 cow_n_col = 1, plot_alignment = 'horizontal')

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.