Plot data in physical space 2D#
Last Updated: Sep 07, 2023
Description#
Visualize cells and feature expression according to spatial coordinates
Usage#
spatFeatPlot2D(
gobject,
feat_type = NULL,
spat_unit = NULL,
show_image = F,
gimage = NULL,
image_name = NULL,
largeImage_name = NULL,
spat_loc_name = NULL,
group_by = NULL,
group_by_subset = NULL,
sdimx = "sdimx",
sdimy = "sdimy",
expression_values = c("normalized", "scaled", "custom"),
feats,
cell_color_gradient = c("blue", "white", "red"),
gradient_midpoint = NULL,
gradient_limits = NULL,
show_network = F,
network_color = NULL,
spatial_network_name = "Delaunay_network",
edge_alpha = NULL,
show_grid = F,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
midpoint = 0,
scale_alpha_with_expression = FALSE,
point_shape = c("border", "no_border", "voronoi"),
point_size = 1,
point_alpha = 1,
point_border_col = "black",
point_border_stroke = 0.1,
show_legend = T,
legend_text = 8,
background_color = "white",
vor_border_color = "white",
vor_alpha = 1,
vor_max_radius = 200,
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 = "spatFeatPlot2D"
)
Arguments#
|
giotto object |
|
feature type |
|
spatial unit |
|
show a tissue background image |
|
a giotto image |
|
name of a giotto image or multiple images if group_by |
|
name of a giottoLargeImage or multiple images if group by |
|
name of spatial locations |
|
create multiple plots based on cell annotation column |
|
subset the group_by factor column |
|
x-axis dimension name (default = ‘sdimx’) |
|
y-axis dimension name (default = ‘sdimy’) |
|
gene expression values to use |
|
features to show |
|
vector with 3 colors for numeric data |
|
midpoint for color gradient |
|
vector with lower and upper limits |
|
show underlying spatial network |
|
color of spatial network |
|
name of spatial network to use |
|
alpha of edge |
|
show spatial grid |
|
color of spatial grid |
|
name of spatial grid to use |
|
expression midpoint |
|
scale expression with ggplot alpha parameter |
|
shape of points (border, no_border or voronoi) |
|
size of point (cell) |
|
transparancy of points |
|
color of border around points |
|
stroke size of border around points |
|
show legend |
|
size of legend text |
|
color of plot background |
|
border colorr for voronoi plot |
|
transparancy of voronoi ‘cells’ |
|
maximum radius for 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 plots |
|
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#
spatGenePlot3D
Other spatial feature expression visualizations:
spatFeatPlot2D_single()