Visualize Gene Expression By Dimension Coordinates¶

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	transparency 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¶

A ggplot.

Details¶

Description of parameters …

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)