Visualize gene expression according to dimension reduction coordinates
dimGenePlot2D( 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, show_NN_network = F, nn_network_to_use = "sNN", network_name = "sNN.pca", network_color = "lightgray", edge_alpha = NULL, scale_alpha_with_expression = FALSE, point_shape = c("border", "no_border"), point_size = 1, point_alpha = 1, cell_color_gradient = c("blue", "white", "red"), gradient_midpoint = NULL, gradient_limits = NULL, point_border_col = "black", point_border_stroke = 0.1, show_legend = T, legend_text = 8, background_color = "white", axis_text = 8, axis_title = 8, cow_n_col = 2, 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 = "dimGenePlot2D" )
Arguments
| 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 |
| 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 |
| edge_alpha | column to use for alpha of the edges |
| scale_alpha_with_expression | scale expression with ggplot alpha parameter |
| point_shape | point with border or not (border or no_border) |
| point_size | size of point (cell) |
| point_alpha | transparancy of points |
| cell_color_gradient | vector with 3 colors for numeric data |
| gradient_midpoint | midpoint for color gradient |
| gradient_limits | vector with lower and upper limits |
| point_border_col | color of border around points |
| point_border_stroke | stroke size of border around points |
| show_legend | show legend |
| legend_text | size of legend text |
| background_color | color of plot background |
| axis_text | size of axis text |
| axis_title | size of axis title |
| 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_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 dimension reduction gene expression visualizations:
dimGenePlot3D(),
dimGenePlot()
Examples
data(mini_giotto_single_cell) all_genes = slot(mini_giotto_single_cell, 'gene_ID') selected_genes = all_genes[1:2] dimGenePlot2D(mini_giotto_single_cell, genes = selected_genes, point_size = 3)
