cellProximityVisPlot#
Last Updated: Jan 14, 2025
Description#
Visualize cell-cell interactions according to spatial coordinates
Usage#
cellProximityVisPlot(
gobject,
interaction_name = NULL,
cluster_column = NULL,
sdimx = NULL,
sdimy = NULL,
sdimz = NULL,
cell_color = NULL,
cell_color_code = NULL,
color_as_factor = T,
show_other_cells = F,
show_network = F,
show_other_network = F,
network_color = NULL,
spatial_network_name = "Delaunay_network",
show_grid = F,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
coord_fix_ratio = 1,
show_legend = T,
point_size_select = 2,
point_select_border_col = "black",
point_select_border_stroke = 0.05,
point_size_other = 1,
point_alpha_other = 0.3,
point_other_border_col = "lightgrey",
point_other_border_stroke = 0.01,
axis_scale = c("cube", "real", "custom"),
custom_ratio = NULL,
x_ticks = NULL,
y_ticks = NULL,
z_ticks = NULL,
plot_method = c("ggplot", "plotly"),
...
)
Arguments#
|
giotto object |
|
cell-cell interaction name |
|
cluster column with cell clusters |
|
x-axis dimension name (default = ‘sdimx’) |
|
y-axis dimension name (default = ‘sdimy’) |
|
z-axis dimension name (default = ‘sdimz’) |
|
color for cells (see details) |
|
named vector with colors |
|
convert color column to factor |
|
show not selected cells |
|
show underlying spatial network |
|
show underlying spatial network of other cells |
|
color of spatial network |
|
name of spatial network to use |
|
show spatial grid |
|
color of spatial grid |
|
name of spatial grid to use |
|
fix ratio between x and y-axis |
|
show legend |
|
size of selected points |
|
border color of selected points |
|
stroke size of selected points |
|
size of other points |
|
alpha of other points |
|
border color of other points |
|
stroke size of other points |
|
scale of axis |
|
custom ratio of scales |
|
x ticks |
|
y ticks |
|
z ticks |
|
method to plot |
|
additional parameters |
Details#
Description of parameters.
Value#
ggplot or plotly