Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode
spatDimGenePlot3D( gobject, expression_values = c("normalized", "scaled", "custom"), plot_alignment = c("horizontal", "vertical"), dim_reduction_to_use = "umap", dim_reduction_name = "umap", dim1_to_use = 1, dim2_to_use = 2, dim3_to_use = NULL, sdimx = "sdimx", sdimy = "sdimy", sdimz = "sdimz", genes, cluster_column = NULL, select_cell_groups = NULL, select_cells = NULL, show_other_cells = T, other_cell_color = "lightgrey", other_point_size = 1.5, show_NN_network = FALSE, nn_network_to_use = "sNN", nn_network_color = "lightgrey", nn_network_alpha = 0.5, network_name = "sNN.pca", label_size = 16, genes_low_color = "blue", genes_mid_color = "white", genes_high_color = "red", dim_point_size = 3, show_spatial_network = FALSE, spatial_network_name = "Delaunay_network", spatial_network_color = "lightgray", spatial_network_alpha = 0.5, show_spatial_grid = FALSE, spatial_grid_name = "spatial_grid", spatial_grid_color = NULL, spatial_grid_alpha = 0.5, spatial_point_size = 3, legend_text_size = 12, axis_scale = c("cube", "real", "custom"), custom_ratio = NULL, x_ticks = NULL, y_ticks = NULL, z_ticks = NULL, show_plot = NA, return_plot = NA, save_plot = NA, save_param = list(), default_save_name = "spatDimGenePlot3D" )
| gobject | giotto object |
|---|---|
| expression_values | gene expression values to use |
| plot_alignment | direction to align plot |
| 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 |
| dim3_to_use | dimension to use on z-axis |
| sdimx | spatial dimension to use on x-axis |
| sdimy | spatial dimension to use on y-axis |
| sdimz | spatial dimension to use on z-axis |
| genes | genes to show |
| cluster_column | cluster column to select groups |
| 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_NN_network | show underlying NN network |
| nn_network_to_use | type of NN network to use (kNN vs sNN) |
| nn_network_color | color of NN network |
| nn_network_alpha | alpha of NN network |
| network_name | name of NN network to use, if show_NN_network = TRUE |
| label_size | size of labels |
| genes_low_color | color for low expression levels |
| genes_mid_color | color for medium expression levels |
| genes_high_color | color for high expression levels |
| dim_point_size | dim reduction plot: point size |
| show_spatial_network | show spatial network (boolean) |
| spatial_network_name | name of spatial network to use |
| spatial_network_color | color of spatial network |
| spatial_network_alpha | alpha of spatial network |
| show_spatial_grid | show spatial grid (boolean) |
| spatial_grid_name | name of spatial grid to use |
| spatial_grid_color | color of spatial grid |
| spatial_grid_alpha | alpha of spatial grid |
| spatial_point_size | spatial plot: point size |
| legend_text_size | size of legend |
| axis_scale | the way to scale the axis |
| custom_ratio | customize the scale of the plot |
| x_ticks | set the number of ticks on the x-axis |
| y_ticks | set the number of ticks on the y-axis |
| z_ticks | set the number of ticks on the z-axis |
| show_plot | show plots |
| return_plot | return plotly 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 |
plotly
Description of parameters.
Other spatial and dimension reduction gene expression visualizations:
spatDimGenePlot2D(),
spatDimGenePlot()