spatCellPlot2D | R Documentation |
Visualize cells according to spatial coordinates
spatCellPlot2D(
gobject,
show_image = F,
gimage = NULL,
image_name = "image",
sdimx = "sdimx",
sdimy = "sdimy",
spat_enr_names = NULL,
cell_annotation_values = NULL,
cell_color_gradient = c("blue", "white", "red"),
gradient_midpoint = NULL,
gradient_limits = NULL,
select_cell_groups = NULL,
select_cells = NULL,
point_shape = c("border", "no_border", "voronoi"),
point_size = 3,
point_alpha = 1,
point_border_col = "black",
point_border_stroke = 0.1,
show_cluster_center = F,
show_center_label = F,
center_point_size = 4,
center_point_border_col = "black",
center_point_border_stroke = 0.1,
label_size = 4,
label_fontface = "bold",
show_network = F,
spatial_network_name = "Delaunay_network",
network_color = NULL,
network_alpha = 1,
show_grid = F,
spatial_grid_name = "spatial_grid",
grid_color = NULL,
show_other_cells = T,
other_cell_color = "lightgrey",
other_point_size = 1,
other_cells_alpha = 0.1,
coord_fix_ratio = NULL,
show_legend = T,
legend_text = 8,
legend_symbol_size = 1,
background_color = "white",
vor_border_color = "white",
vor_max_radius = 200,
vor_alpha = 1,
axis_text = 8,
axis_title = 8,
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 = "spatCellPlot2D"
)
gobject |
giotto object |
show_image |
show a tissue background image |
gimage |
a giotto image |
image_name |
name of a giotto image |
sdimx |
x-axis dimension name (default = 'sdimx') |
sdimy |
y-axis dimension name (default = 'sdimy') |
spat_enr_names |
names of spatial enrichment results to include |
cell_annotation_values |
numeric cell annotation columns |
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 |
point_shape |
shape of points (border, no_border or voronoi) |
point_size |
size of point (cell) |
point_alpha |
transparancy of spatial points |
point_border_col |
color of border around points |
point_border_stroke |
stroke size of border around points |
show_cluster_center |
plot center of selected clusters |
show_center_label |
plot label of selected clusters |
center_point_size |
size of center points |
center_point_border_col |
border color of center points |
center_point_border_stroke |
border stroke size of center points |
label_size |
size of labels |
label_fontface |
font of labels |
show_network |
show underlying spatial network |
spatial_network_name |
name of spatial network to use |
network_color |
color of spatial network |
network_alpha |
alpha of spatial network |
show_grid |
show spatial grid |
spatial_grid_name |
name of spatial grid to use |
grid_color |
color of spatial grid |
show_other_cells |
display not selected cells |
other_cell_color |
color of not selected cells |
other_point_size |
point size of not selected cells |
other_cells_alpha |
alpha of not selected cells |
coord_fix_ratio |
fix ratio between x and y-axis |
show_legend |
show legend |
legend_text |
size of legend text |
legend_symbol_size |
size of legend symbols |
background_color |
color of plot background |
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 |
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 |
default_save_name |
default save name for saving, don't change, change save_name in save_param |
Description of parameters.
ggplot
Other spatial cell annotation visualizations:
spatCellPlot()
data(mini_giotto_single_cell)
# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')
# visualize total expression information
spatCellPlot2D(mini_giotto_single_cell, cell_annotation_values = 'total_expr')
# visualize enrichment results
spatCellPlot2D(mini_giotto_single_cell,
spat_enr_names = 'cluster_metagene',
cell_annotation_values = c('1','2'))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.