Visualize numerical features of cells according to spatial AND dimension reduction coordinates in 2D
spatDimCellPlot2D(
gobject,
show_image = F,
gimage = NULL,
image_name = "image",
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"
)giotto object
show a tissue background image
a giotto image
name of a giotto image
direction to align plot
names of spatial enrichment results to include
numeric cell annotation columns
dimension reduction to use
dimension reduction name
dimension to use on x-axis
dimension to use on y-axis
= spatial dimension to use on x-axis
= spatial dimension to use on y-axis
vector with 3 colors for numeric data
midpoint for color gradient
vector with lower and upper limits
select subset of cells/clusters based on cell_color parameter
select subset of cells based on cell IDs
dim reduction points with border or not (border or no_border)
size of points in dim. reduction space
transparancy of dim. reduction points
border color of points in dim. reduction space
border stroke of points in dim. reduction space
shape of points (border, no_border or voronoi)
size of spatial points
transparancy of spatial points
border color of spatial points
border stroke of spatial points
show the center of each cluster
provide a label for each cluster
size of the center point
border color of center point
stroke size of center point
size of the center label
font of the center label
show the center of each cluster
provide a label for each cluster
size of the spatial center points
border color of the spatial center points
stroke size of the spatial center points
size of the center label
font of the center label
show underlying NN network
type of NN network to use (kNN vs sNN)
name of NN network to use, if show_NN_network = TRUE
column to use for alpha of the edges
show spatial network
name of spatial network to use
color of spatial network
alpha of spatial network
show spatial grid
name of spatial grid to use
color of spatial grid
display not selected cells
color of not selected cells
size of not selected dim cells
size of not selected spat cells
alpha of not selected spat cells
show legend
size of legend text
size of legend symbols
background color of points in dim. reduction space
background color of spatial points
border colorr for voronoi plot
maximum radius for voronoi 'cells'
transparancy of voronoi 'cells'
size of axis text
size of axis title
ratio for coordinates
cowplot param: how many columns
cowplot param: relative height
cowplot param: relative width
cowplot param: how to align
show plot
return ggplot object
directly save the plot [boolean]
list of saving parameters, see showSaveParameters
default save name for saving, don't change, change save_name in save_param
ggplot
Description of parameters.
Other spatial and dimension reduction cell annotation visualizations:
spatDimCellPlot()
data(mini_giotto_single_cell)
# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')
# visualize total expression information
spatDimCellPlot2D(mini_giotto_single_cell, cell_annotation_values = 'total_expr')
# visualize enrichment results
spatDimCellPlot2D(mini_giotto_single_cell,
spat_enr_names = 'cluster_metagene',
cell_annotation_values = c('1','2'))