Visualize cells according to spatial AND dimension reduction coordinates 2D
spatDimPlot(...)
Arguments passed on to spatDimPlot2D
gobject
giotto object
show_image
show a tissue background image
gimage
a giotto image
image_name
name of a giotto image
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
ggplot
Description of parameters.
spatDimPlot2D
and spatDimPlot3D
for 3D visualization.
Other spatial and dimension reduction visualizations:
spatDimPlot2D()
,
spatDimPlot3D()
data(mini_giotto_single_cell)
spatDimPlot(mini_giotto_single_cell)
spatDimPlot(mini_giotto_single_cell, cell_color = 'cell_types',
spat_point_size = 3, dim_point_size = 3)