gobject
giotto object
spat_unit
spatial unit
feat_type
feature type
show_image
show a tissue background image
gimage
a giotto image
image_name
name of a giotto image or
multiple images with group_by
largeImage_name
name of a giottoLargeImage or
multiple images with group_by
group_by
create multiple plots based on
cell annotation column
group_by_subset
subset the group_by factor
column
spat_loc_name
name of spatial locations
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_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
point_shape
shape of points (border,
no_border or voronoi)
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
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
(default = 1)
title
title of plot
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
showSaveParameters
default_save_name
default save name for saving,
don’t change, change save_name
in save_param