spatDimPlot#

Last Updated: Jan 29, 2024

Description#

Visualize cells according to spatial AND dimension reduction coordinates 2D

Usage#

spatDimPlot(...)

Arguments#

...

Arguments passed on to spatDimPlot2D

gobject: giotto object
spat_unit: spatial unit
feat_type: feature type
show_image: show a tissue background image
gimage: a giotto image
image_name: name of a giotto image
largeImage_name: name of a giottoLargeImage
spat_loc_name: name of spatial locations
plot_alignment: direction to align plot
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
spat_enr_names: names of spatial enrichment results to include
cell_color: color for cells (see details)
color_as_factor: convert color column to factor
cell_color_code: named vector with colors
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: point with border or not (border or no_border)
dim_point_size: size of points in dim. reduction space
dim_point_alpha: transparancy of point in dim. reduction space
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 center point
spat_center_point_border_col: border color of spatial center points

``spat_center_point_border_stroke ``

border strike size of 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)
network_name: name of NN network to use, if show_NN_network = TRUE
nn_network_alpha: column to use for alpha of the edges
show_spatial_network: show spatial network
spat_network_name: name of spatial network to use
spat_network_color: color of spatial network
spat_network_alpha: alpha of spatial network
show_spatial_grid: show spatial grid
spat_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
dim_show_legend: show legend of dimension reduction plot
spat_show_legend: show legend of spatial plot
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
show_plot: show plot
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