Visualize cells and gene expression according to dimension reduction coordinates
dimGenePlot3D( gobject, expression_values = c("normalized", "scaled", "custom"), genes = NULL, dim_reduction_to_use = "umap", dim_reduction_name = "umap", dim1_to_use = 1, dim2_to_use = 2, dim3_to_use = 3, show_NN_network = F, nn_network_to_use = "sNN", network_name = "sNN.pca", network_color = "lightgray", cluster_column = NULL, select_cell_groups = NULL, select_cells = NULL, show_other_cells = T, other_cell_color = "lightgrey", other_point_size = 1, edge_alpha = NULL, point_size = 2, genes_high_color = NULL, genes_mid_color = "white", genes_low_color = "blue", show_legend = T, show_plot = NA, return_plot = NA, save_plot = NA, save_param = list(), default_save_name = "dimGenePlot3D" )
| gobject | giotto object |
|---|---|
| expression_values | gene expression values to use |
| 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 |
| dim3_to_use | dimension to use on z-axis |
| show_NN_network | show underlying 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 |
| network_color | color of NN network |
| 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 |
| edge_alpha | column to use for alpha of the edges |
| point_size | size of point (cell) |
| genes_high_color | color for high expression levels |
| genes_mid_color | color for medium expression levels |
| genes_low_color | color for low expression levels |
| show_legend | show legend |
| 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 |
ggplot
Description of parameters.
Other dimension reduction gene expression visualizations:
dimGenePlot2D(),
dimGenePlot()