Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode
spatDimGenePlot2D( gobject, show_image = F, gimage = NULL, image_name = "image", expression_values = c("normalized", "scaled", "custom"), plot_alignment = c("vertical", "horizontal"), genes, 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 = 2, cow_rel_h = 1, cow_rel_w = 1, cow_align = "h", show_legend = T, legend_text = 8, 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 = "spatDimGenePlot2D" )
Arguments
| gobject | giotto object |
|---|---|
| show_image | show a tissue background image |
| gimage | a giotto image |
| image_name | name of a giotto image |
| expression_values | gene expression values to use |
| plot_alignment | direction to align plot |
| genes | genes to show |
| dim_reduction_to_use | dimension reduction to use |
| dim_reduction_name | dimension reduction name |
| dim1_to_use | dimension to use on x-axis |
| dim2_to_use | dimension to use on y-axis |
| dim_point_shape | dim reduction points with border or not (border or no_border) |
| dim_point_size | dim reduction plot: point size |
| dim_point_alpha | transparancy of dim. reduction points |
| dim_point_border_col | color of border around points |
| dim_point_border_stroke | stroke size of border around points |
| show_NN_network | show underlying NN network |
| show_spatial_network | show underlying spatial netwok |
| dim_network_color | color of 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 |
| dim_edge_alpha | dim reduction plot: column to use for alpha of the edges |
| scale_alpha_with_expression | scale expression with ggplot alpha parameter |
| sdimx | spatial x-axis dimension name (default = 'sdimx') |
| sdimy | spatial y-axis dimension name (default = 'sdimy') |
| spatial_network_name | name of spatial network to use |
| spatial_network_color | color of spatial network |
| show_spatial_grid | show spatial grid |
| grid_color | color of spatial grid |
| spatial_grid_name | name of spatial grid to use |
| spat_point_shape | spatial points with border or not (border or no_border) |
| spat_point_size | spatial plot: point size |
| spat_point_alpha | transparancy of spatial points |
| spat_point_border_col | color of border around points |
| spat_point_border_stroke | stroke size of border around points |
| spat_edge_alpha | edge alpha |
| cell_color_gradient | vector with 3 colors for numeric data |
| gradient_midpoint | midpoint for color gradient |
| gradient_limits | vector with lower and upper limits |
| 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_legend | show legend |
| legend_text | size of legend text |
| dim_background_color | color of plot background for dimension plot |
| spat_background_color | color of plot background for spatial plot |
| 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 |
| show_plot | show plots |
| return_plot | return ggplot object |
| save_plot | directly save the plot [boolean] |
| save_param | list of saving parameters, see |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
Value
ggplot
Details
Description of parameters.
See also
Other spatial and dimension reduction gene expression visualizations:
spatDimGenePlot3D(),
spatDimGenePlot()
Examples
data(mini_giotto_single_cell) all_genes = slot(mini_giotto_single_cell, 'gene_ID') selected_genes = all_genes[1] spatDimGenePlot2D(mini_giotto_single_cell, genes = selected_genes, dim_point_size = 3, spat_point_size = 3, cow_n_col = 1, plot_alignment = 'horizontal')
