spatDimPlot2D | R Documentation |
Visualize cells according to spatial AND dimension reduction coordinates 2D
spatDimPlot2D(
gobject,
show_image = F,
gimage = NULL,
image_name = "image",
plot_alignment = c("vertical", "horizontal"),
dim_reduction_to_use = "umap",
dim_reduction_name = "umap",
dim1_to_use = 1,
dim2_to_use = 2,
sdimx = "sdimx",
sdimy = "sdimy",
spat_enr_names = NULL,
cell_color = NULL,
color_as_factor = T,
cell_color_code = NULL,
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 = "blue",
spat_center_point_border_stroke = 0.1,
spat_label_size = 4,
spat_label_fontface = "bold",
show_NN_network = F,
nn_network_to_use = "sNN",
network_name = "sNN.pca",
nn_network_alpha = 0.05,
show_spatial_network = F,
spat_network_name = "Delaunay_network",
spat_network_color = "blue",
spat_network_alpha = 0.5,
show_spatial_grid = F,
spat_grid_name = "spatial_grid",
spat_grid_color = "blue",
show_other_cells = T,
other_cell_color = "lightgrey",
dim_other_point_size = 1,
spat_other_point_size = 1,
spat_other_cells_alpha = 0.5,
dim_show_legend = F,
spat_show_legend = F,
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,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "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 |
default_save_name |
default save name for saving, don't change, change save_name in save_param |
Description of parameters.
ggplot
spatDimPlot3D
Other spatial and dimension reduction visualizations:
spatDimPlot3D()
,
spatDimPlot()
data(mini_giotto_single_cell)
spatDimPlot2D(mini_giotto_single_cell)
spatDimPlot2D(mini_giotto_single_cell, cell_color = 'cell_types',
spat_point_size = 3, dim_point_size = 3)
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