spatDimFeatPlot2D#
Last Updated: Jan 14, 2025
Description#
Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode
Usage#
spatDimFeatPlot2D(
gobject,
spat_unit = NULL,
feat_type = NULL,
show_image = F,
gimage = NULL,
image_name = NULL,
largeImage_name = NULL,
expression_values = c("normalized", "scaled", "custom"),
plot_alignment = c("vertical", "horizontal"),
feats,
dim_reduction_to_use = "umap",
dim_reduction_name = "umap",
dim1_to_use = 1,
dim2_to_use = 2,
dim_point_shape = c("border", "no_border"),
dim_point_size = 1,
dim_point_alpha = 1,
dim_point_border_col = "black",
dim_point_border_stroke = 0.1,
show_NN_network = F,
show_spatial_network = F,
dim_network_color = "gray",
nn_network_to_use = "sNN",
network_name = "sNN.pca",
dim_edge_alpha = NULL,
scale_alpha_with_expression = FALSE,
sdimx = "sdimx",
sdimy = "sdimy",
spatial_network_name = "Delaunay_network",
spatial_network_color = NULL,
show_spatial_grid = F,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
spat_point_shape = c("border", "no_border", "voronoi"),
spat_point_size = 1,
spat_point_alpha = 1,
spat_point_border_col = "black",
spat_point_border_stroke = 0.1,
spat_edge_alpha = NULL,
cell_color_gradient = c("blue", "white", "red"),
gradient_midpoint = NULL,
gradient_limits = NULL,
cow_n_col = NULL,
cow_rel_h = 1,
cow_rel_w = 1,
cow_align = "h",
show_legend = TRUE,
legend_text = 10,
dim_background_color = "white",
spat_background_color = "white",
vor_border_color = "white",
vor_max_radius = 200,
vor_alpha = 1,
axis_text = 8,
axis_title = 8,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "spatDimFeatPlot2D"
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
show a tissue background image |
|
a giotto image |
|
name of a giotto image |
|
name of a giottoLargeImage |
|
feat expression values to use |
|
direction to align plot |
|
features to show |
|
dimension reduction to use |
|
dimension reduction name |
|
dimension to use on x-axis |
|
dimension to use on y-axis |
|
dim reduction points with border or not (border or no_border) |
|
dim reduction plot: point size |
|
transparancy of dim. reduction points |
|
color of border around points |
|
stroke size of border around points |
|
show underlying NN network |
|
show underlying spatial netwok |
|
color of NN network |
|
type of NN network to use (kNN vs sNN) |
|
name of NN network to use, if show_NN_network = TRUE |
|
dim reduction plot: column to use for alpha of the edges |
|
scale expression with ggplot alpha parameter |
|
spatial x-axis dimension name (default = ‘sdimx’) |
|
spatial y-axis dimension name (default = ‘sdimy’) |
|
name of spatial network to use |
|
color of spatial network |
|
show spatial grid |
|
color of spatial grid |
|
name of spatial grid to use |
|
spatial points with border or not (border or no_border) |
|
spatial plot: point size |
|
transparancy of spatial points |
|
color of border around points |
|
stroke size of border around points |
|
edge alpha |
|
vector with 3 colors for numeric data |
|
midpoint for color gradient |
|
vector with lower and upper limits |
|
cowplot param: how many columns |
|
cowplot param: relative height |
|
cowplot param: relative width |
|
cowplot param: how to align |
|
show legend |
|
size of legend text |
|
color of plot background for dimension plot |
|
color of plot background for spatial plot |
|
border colorr for voronoi plot |
|
maximum radius for voronoi ‘cells’ |
|
transparancy of voronoi ‘cells’ |
|
size of axis text |
|
size of axis title |
|
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