dimGenePlot

Visualize gene expression according to dimension reduction coordinates

dimGenePlot(...)

Arguments

...

Arguments passed on to dimGenePlot2D 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 showSaveParameters 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

dimGenePlot3D

Other dimension reduction gene expression visualizations: dimGenePlot2D(), dimGenePlot3D()

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
dimGenePlot(mini_giotto_single_cell, genes = selected_genes, point_size = 3)