spatDimGenePlot

Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode

spatDimGenePlot(...)

Arguments

...

Arguments passed on to spatDimGenePlot2D

gobject: giotto object
show_image: show a tissue background image
gimage: a giotto image
image_name: name of a giotto image
expression_values: gene expression values to use
plot_alignment: direction to align plot
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
dim_point_shape: dim reduction points with border or not (border or no_border)
dim_point_size: dim reduction plot: point size
dim_point_alpha: transparancy of dim. reduction points
dim_point_border_col: color of border around points
dim_point_border_stroke: stroke size of border around points
show_NN_network: show underlying NN network
show_spatial_network: show underlying spatial netwok
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
dim_network_color: color of NN network
dim_edge_alpha: dim reduction plot: column to use for alpha of the edges
scale_alpha_with_expression: scale expression with ggplot alpha parameter
sdimx: spatial x-axis dimension name (default = 'sdimx')
sdimy: spatial y-axis dimension name (default = 'sdimy')
spatial_network_name: name of spatial network to use
spatial_network_color: color of spatial network
show_spatial_grid: show spatial grid
grid_color: color of spatial grid
spatial_grid_name: name of spatial grid to use
spat_point_shape: spatial points with border or not (border or no_border)
spat_point_size: spatial plot: point size
spat_point_alpha: transparancy of spatial points
spat_point_border_col: color of border around points
spat_point_border_stroke: stroke size of border around points
spat_edge_alpha: edge alpha
cell_color_gradient: vector with 3 colors for numeric data
gradient_midpoint: midpoint for color gradient
gradient_limits: vector with lower and upper limits
show_legend: show legend
legend_text: size of legend text
dim_background_color: color of plot background for dimension plot
spat_background_color: color of plot background for spatial plot
vor_border_color: border colorr for voronoi plot
vor_max_radius: maximum radius for voronoi 'cells'
vor_alpha: transparancy of voronoi 'cells'
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.

Examples


data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1]
spatDimGenePlot(mini_giotto_single_cell, genes = selected_genes,
                 dim_point_size = 3, spat_point_size = 3,
                 cow_n_col = 1, plot_alignment = 'horizontal')

Arguments

Value

Details

See also

Examples