dimGenePlot2D: dimGenePlot2D

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

dimGenePlot2D

Description

Visualize gene expression according to dimension reduction coordinates

Usage

dimGenePlot2D(gobject, genes = NULL, default_save_name = "dimGenePlot2D", ...)

Arguments

gobject	giotto object
genes	genes to show
default_save_name	default save name for saving, don't change, change save_name in save_param
...	Arguments passed on to dimFeatPlot2D feat_type feature type spat_unit spatial unit expression_values gene expression values to use order order points according to feature expression 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

Details

Description of parameters.

Value

ggplot

See Also

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.