spatCellPlot2D#
Last Updated: Oct 02, 2023
Description#
Visualize cells according to spatial coordinates
Usage#
spatCellPlot2D(
gobject,
spat_unit = NULL,
feat_type = NULL,
show_image = F,
gimage = NULL,
image_name = NULL,
largeImage_name = NULL,
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 = 1,
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 = NULL,
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"
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
show a tissue background image |
|
a giotto image |
|
name of a giotto image |
|
name of a giottoLargeImage |
|
x-axis dimension name (default = ‘sdimx’) |
|
y-axis dimension name (default = ‘sdimy’) |
|
names of spatial enrichment results to include |
|
numeric cell annotation columns |
|
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 |
|
shape of points (border, no_border or voronoi) |
|
size of point (cell) |
|
transparancy of spatial points |
|
color of border around points |
|
stroke size of border around points |
|
plot center of selected clusters |
|
plot label of selected clusters |
|
size of center points |
|
border color of center points |
|
border stroke size of center points |
|
size of labels |
|
font of labels |
|
show underlying 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 |
|
point size of not selected cells |
|
alpha of not selected cells |
|
fix ratio between x and y-axis |
|
show legend |
|
size of legend text |
|
size of legend symbols |
|
color of plot background |
|
border colorr for voronoi plot |
|
maximum radius for voronoi ‘cells’ |
|
transparancy of voronoi ‘cells’ |
|
size of axis text |
|
size of axis title |
|
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
|
|
default save name for saving, don’t change, change save_name in save_param |
Details#
Description of parameters.
Value#
ggplot
See Also#
Other spatial cell annotation visualizations: spatCellPlot()