spat_unit
spatial unit
feat_type
feature type
group_by
create multiple plots based on
cell annotation column
group_by_subset
subset the group_by factor
column
dim1_to_use
dimension to use on x-axis
dim2_to_use
dimension to use on y-axis
spat_enr_names
names of spatial enrichment
results to include
show_NN_network
show underlying NN network
nn_network_to_use
type of NN network to use (kNN
vs sNN)
network_name
name of NN network to use, if
show_NN_network = TRUE
cell_color
color for cells (see details)
color_as_factor
convert color column to factor
cell_color_code
named vector with colors
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
show_other_cells
display not selected cells
other_cell_color
color of not selected cells
other_point_size
size of not selected cells
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
edge_alpha
column to use for alpha of the
edges
point_shape
point with border or not
(border or no_border)
point_size
size of point (cell)
point_alpha
transparancy of point
point_border_col
color of border around points
point_border_stroke
stroke size of border around
points
title
title for plot, defaults to
cell_color parameter
show_legend
show legend
legend_text
size of legend text
legend_symbol_size
size of legend symbols
background_color
color of plot background
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
heights of rows (e.g. c(1,2))
cow_rel_w
cowplot param: relative widths
of columns (e.g. c(1,2))
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
showSaveParameters