spatDimCellPlot2D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L6204

Description#

Visualize numerical features of cells according to spatial AND dimension reduction coordinates in 2D

Usage#

spatDimCellPlot2D(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  show_image = F,
  gimage = NULL,
  image_name = NULL,
  largeImage_name = NULL,
  plot_alignment = c("vertical", "horizontal"),
  spat_enr_names = NULL,
  cell_annotation_values = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  sdimx = "sdimx",
  sdimy = "sdimy",
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  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,
  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,
  dim_show_cluster_center = F,
  dim_show_center_label = T,
  dim_center_point_size = 4,
  dim_center_point_border_col = "black",
  dim_center_point_border_stroke = 0.1,
  dim_label_size = 4,
  dim_label_fontface = "bold",
  spat_show_cluster_center = F,
  spat_show_center_label = F,
  spat_center_point_size = 4,
  spat_center_point_border_col = "black",
  spat_center_point_border_stroke = 0.1,
  spat_label_size = 4,
  spat_label_fontface = "bold",
  show_NN_network = F,
  nn_network_to_use = "sNN",
  nn_network_name = "sNN.pca",
  dim_edge_alpha = 0.5,
  spat_show_network = F,
  spatial_network_name = "Delaunay_network",
  spat_network_color = "red",
  spat_network_alpha = 0.5,
  spat_show_grid = F,
  spatial_grid_name = "spatial_grid",
  spat_grid_color = "green",
  show_other_cells = TRUE,
  other_cell_color = "grey",
  dim_other_point_size = 0.5,
  spat_other_point_size = 0.5,
  spat_other_cells_alpha = 0.5,
  show_legend = T,
  legend_text = 8,
  legend_symbol_size = 1,
  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,
  coord_fix_ratio = NULL,
  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 = "spatDimCellPlot2D"
)

Arguments#

Argument

Description

gobject

giotto object

feat_type

feature type

spat_unit

spatial unit

show_image

show a tissue background image

gimage

a giotto image

image_name

name of a giotto image

largeImage_name

name of a giottoLargeImage

plot_alignment

direction to align plot

spat_enr_names

names of spatial enrichment results to include

cell_annotation_values

numeric cell annotation columns

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

sdimx

= spatial dimension to use on x-axis

sdimy

= spatial dimension to use on y-axis

cell_color_gradient

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

select_cell_groups

select subset of cells/clusters based on cell_color parameter

select_cells

select subset of cells based on cell IDs

dim_point_shape

dim reduction points with border or not (border or no_border)

dim_point_size

size of points in dim. reduction space

dim_point_alpha

transparancy of dim. reduction points

dim_point_border_col

border color of points in dim. reduction space

dim_point_border_stroke

border stroke of points in dim. reduction space

spat_point_shape

shape of points (border, no_border or voronoi)

spat_point_size

size of spatial points

spat_point_alpha

transparancy of spatial points

spat_point_border_col

border color of spatial points

spat_point_border_stroke

border stroke of spatial points

dim_show_cluster_center

show the center of each cluster

dim_show_center_label

provide a label for each cluster

dim_center_point_size

size of the center point

`` dim_center_point_border_col``

border color of center point

dim _center_point_border_stroke

stroke size of center point

dim_label_size

size of the center label

dim_label_fontface

font of the center label

spat_show_cluster_center

show the center of each cluster

spat_show_center_label

provide a label for each cluster

spat_center_point_size

size of the spatial center points

s pat_center_point_border_col

border color of the spatial center points

spat _center_point_border_stroke

stroke size of the spatial center points

spat_label_size

size of the center label

spat_label_fontface

font of the center label

show_NN_network

show underlying NN network

nn_network_to_use

type of NN network to use (kNN vs sNN)

nn_network_name

name of NN network to use, if show_NN_network = TRUE

dim_edge_alpha

column to use for alpha of the edges

spat_show_network

show spatial network

spatial_network_name

name of spatial network to use

spat_network_color

color of spatial network

spat_network_alpha

alpha of spatial network

spat_show_grid

show spatial grid

spatial_grid_name

name of spatial grid to use

spat_grid_color

color of spatial grid

show_other_cells

display not selected cells

other_cell_color

color of not selected cells

dim_other_point_size

size of not selected dim cells

spat_other_point_size

size of not selected spat cells

spat_other_cells_alpha

alpha of not selected spat cells

show_legend

show legend

legend_text

size of legend text

legend_symbol_size

size of legend symbols

dim_background_color

background color of points in dim. reduction space

spat_background_color

background color of spatial points

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

coord_fix_ratio

ratio for coordinates

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 plot

return_plot

return ggplot object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters, see `showSaveP arameters <#showsaveparameters>`__

default_save_name

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

Details#

Description of parameters.

Value#

ggplot

Seealso#

Other spatial and dimension reduction cell annotation visualizations: `spatDimCellPlot <#spatdimcellplot>`__