View source: R/spatial_interaction_visuals.R
cellProximityVisPlot | R Documentation |
Visualize cell-cell interactions according to spatial coordinates
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"),
...
)
gobject |
giotto object |
interaction_name |
cell-cell interaction name |
cluster_column |
cluster column with cell clusters |
sdimx |
x-axis dimension name (default = 'sdimx') |
sdimy |
y-axis dimension name (default = 'sdimy') |
sdimz |
z-axis dimension name (default = 'sdimz') |
cell_color |
color for cells (see details) |
cell_color_code |
named vector with colors |
color_as_factor |
convert color column to factor |
show_other_cells |
show not selected cells |
show_network |
show underlying spatial network |
show_other_network |
show underlying spatial network of other cells |
network_color |
color of spatial network |
spatial_network_name |
name of spatial network to use |
show_grid |
show spatial grid |
grid_color |
color of spatial grid |
spatial_grid_name |
name of spatial grid to use |
coord_fix_ratio |
fix ratio between x and y-axis |
show_legend |
show legend |
point_size_select |
size of selected points |
point_select_border_col |
border color of selected points |
point_select_border_stroke |
stroke size of selected points |
point_size_other |
size of other points |
point_alpha_other |
alpha of other points |
point_other_border_col |
border color of other points |
point_other_border_stroke |
stroke size of other points |
axis_scale |
scale of axis |
custom_ratio |
custom ratio of scales |
x_ticks |
x ticks |
y_ticks |
y ticks |
z_ticks |
z ticks |
plot_method |
method to plot |
... |
additional parameters |
Description of parameters.
ggplot or plotly
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