Visualize gene expression according to dimension reduction coordinates
dimGenePlot(...)Arguments passed on to dimGenePlot2D
gobjectgiotto object
expression_valuesgene expression values to use
genesgenes to show
dim_reduction_to_usedimension reduction to use
dim_reduction_namedimension reduction name
dim1_to_usedimension to use on x-axis
dim2_to_usedimension to use on y-axis
show_NN_networkshow underlying NN network
nn_network_to_usetype of NN network to use (kNN vs sNN)
network_namename of NN network to use, if show_NN_network = TRUE
network_colorcolor of NN network
edge_alphacolumn to use for alpha of the edges
scale_alpha_with_expressionscale expression with ggplot alpha parameter
point_shapepoint with border or not (border or no_border)
point_sizesize of point (cell)
point_alphatransparancy of points
cell_color_gradientvector with 3 colors for numeric data
gradient_midpointmidpoint for color gradient
gradient_limitsvector with lower and upper limits
point_border_colcolor of border around points
point_border_strokestroke size of border around points
show_legendshow legend
legend_textsize of legend text
background_colorcolor of plot background
axis_textsize of axis text
axis_titlesize of axis title
cow_n_colcowplot param: how many columns
cow_rel_hcowplot param: relative height
cow_rel_wcowplot param: relative width
cow_aligncowplot param: how to align
show_plotshow plots
return_plotreturn ggplot object
save_plotdirectly save the plot [boolean]
save_paramlist of saving parameters, see showSaveParameters
default_save_namedefault save name for saving, don't change, change save_name in save_param
ggplot
Description of parameters.
Other dimension reduction gene expression visualizations:
dimGenePlot2D(),
dimGenePlot3D()
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)