Visualize Features of Cells By Spatial And Dimension Coordinates in 2D

spatDimCellPlot2D()

Visualize numerical features of cells according to spatial AND dimension reduction coordinates in 2D

spatDimCellPlot2D(
    gobject,
    show_image = F,
    gimage = NULL,
    image_name = "image",
    plot_alignment = c("vertical", "horizontal"),
    spat_enr_names = NULL,
    cell_annotation_values = NULL,
    dim_reduction_to_use = "umap",
    dim_reduction_name = "umap",
    dim1_to_use = 1,
    dim2_to_use = 2,
    sdimx = "sdimx",
    sdimy = "sdimy",
    cell_color_gradient = c("blue", "white", "red"),
    gradient_midpoint = NULL,
    gradient_limits = NULL,
    select_cell_groups = NULL,
    select_cells = NULL,
    dim_point_shape = c("border", "no_border"),
    dim_point_size = 1,
    dim_point_alpha = 1,
    dim_point_border_col = "black",
    dim_point_border_stroke = 0.1,
    spat_point_shape = c("border", "no_border", "voronoi"),
    spat_point_size = 1,
    spat_point_alpha = 1,
    spat_point_border_col = "black",
    spat_point_border_stroke = 0.1,
    dim_show_cluster_center = F,
    dim_show_center_label = T,
    dim_center_point_size = 4,
    dim_center_point_border_col = "black",
    dim_center_point_border_stroke = 0.1,
    dim_label_size = 4,
    dim_label_fontface = "bold",
    spat_show_cluster_center = F,
    spat_show_center_label = F,
    spat_center_point_size = 4,
    spat_center_point_border_col = "black",
    spat_center_point_border_stroke = 0.1,
    spat_label_size = 4,
    spat_label_fontface = "bold",
    show_NN_network = F,
    nn_network_to_use = "sNN",
    nn_network_name = "sNN.pca",
    dim_edge_alpha = 0.5,
    spat_show_network = F,
    spatial_network_name = "Delaunay_network",
    spat_network_color = "red",
    spat_network_alpha = 0.5,
    spat_show_grid = F,
    spatial_grid_name = "spatial_grid",
    spat_grid_color = "green",
    show_other_cells = TRUE,
    other_cell_color = "grey",
    dim_other_point_size = 0.5,
    spat_other_point_size = 0.5,
    spat_other_cells_alpha = 0.5,
    show_legend = T,
    legend_text = 8,
    legend_symbol_size = 1,
    dim_background_color = "white",
    spat_background_color = "white",
    vor_border_color = "white",
    vor_max_radius = 200,
    vor_alpha = 1,
    axis_text = 8,
    axis_title = 8,
    coord_fix_ratio = NULL,
    cow_n_col = 2,
    cow_rel_h = 1,
    cow_rel_w = 1,
    cow_align = "h",
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "spatDimCellPlot2D"
)

Arguments

gobject	giotto object
show_image	show a tissue background image
gimage	a giotto image
image_name	name of a giotto image
plot_alignment	direction to align plot
spat_enr_names	names of spatial enrichment results to include
cell_annotation_values	numeric cell annotation columns
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
sdimx	= spatial dimension to use on x-axis
sdimy	= spatial dimension to use on y-axis
cell_color_gradient	vector with 3 colors for numeric data
gradient_midpoint	midpoint for color gradient
gradient_limits	vector with lower and upper limits
select_cell_groups	select subset of cells/clusters based on cell_color parameter
select_cells	select subset of cells based on cell IDs
dim_point_shape	dim reduction points with border or not (border or no_border)
dim_point_size	size of points in dim. reduction space
dim_point_alpha	transparency of dim. reduction points
dim_point_border_col	border color of points in dim. reduction space
dim_point_border_stroke	border stroke of points in dim. reduction space
spat_point_shape	shape of points (border, no_border or voronoi)
spat_point_size	size of spatial points
spat_point_alpha	transparency of spatial points
spat_point_border_col	border color of spatial points
spat_point_border_stroke	border stroke of spatial points
dim_show_cluster_center	show the center of each cluster
dim_show_center_label	provide a label for each cluster
dim_center_point_size	size of the center point
dim_center_point_border_col	border color of center point
dim_center_point_border_stroke	stroke size of center point
dim_label_size	size of the center label
dim_label_fontface	font of the center label
spat_show_cluster_center	show the center of each cluster
spat_show_center_label	provide a label for each cluster
spat_center_point_size	size of the spatial center points
spat_center_point_border_col	border color of the spatial center points
spat_center_point_border_stroke	stroke size of the spatial center points
spat_label_size	size of the center label
spat_label_fontface	font of the center label
show_NN_network	show underlying NN network
nn_network_to_use	type of NN network to use (kNN vs sNN)
nn_network_name	name of NN network to use, if show_NN_network = TRUE
dim_edge_alpha	column to use for alpha of the edges
spat_show_network	show spatial network
spatial_network_name	name of spatial network to use
spat_network_color	color of spatial network
spat_network_alpha	alpha of spatial network
spat_show_grid	show spatial grid
spatial_grid_name	name of spatial grid to use
spat_grid_color	color of spatial grid
show_other_cells	display not selected cells
other_cell_color	color of not selected cells
dim_other_point_size	size of not selected dim cells
spat_other_point_size	size of not selected spat cells
spat_other_cells_alpha	alpha of not selected spat cells
coord_fix_ratio	ratio for coordinates
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_legend	show legend
legend_text	size of legend text
legend_symbol_size	size of legend symbols
dim_background_color	background color of points in dim. reduction space
spat_background_color	background color of spatial points
vor_border_color	border color for voronoi plot
vor_max_radius	maximum radius for voronoi ‘cells’
vor_alpha	transparency of voronoi ‘cells’
axis_text	size of axis text
axis_title	size of axis title
show_plot	show plot
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 …

See also

For other spatial and dimension reduction cell annotation visualizations see: spatDimCellPlot().

Examples

data(mini_giotto_single_cell)

# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')
#>      cell_ID nr_genes perc_genes total_expr leiden_clus cell_types   sdimx
#>  1:   cell_2       13         65  111.98320           3     cell C 1589.47
#>  2:   cell_7       15         75  115.73030           3     cell C 1291.34
#>  3:  cell_12       11         55   95.49802           1     cell A 1183.07
#>  4:  cell_15       12         60   99.94782           3     cell C 1115.86
#>  5:  cell_17       13         65  111.32963           2     cell B 1074.92
#>  6:  cell_30       11         55   96.64302           3     cell C  882.00
#>  7:  cell_37        6         30   57.77777           2     cell B  618.20
#>  8:  cell_40        9         45   82.84693           2     cell B  565.40
#>  9:  cell_44        9         45   79.93838           2     cell B  417.40
#> 10:  cell_53        9         45   82.40747           1     cell A 1831.19
#> 11:  cell_64        8         40   73.06345           1     cell A 1839.07
#> 12:  cell_74       11         55   93.04295           3     cell C 1575.84
#> 13:  cell_85        8         40   73.72574           1     cell A 1440.75
#> 14:  cell_86       14         70  115.75186           1     cell A 1427.06
#> 15:  cell_90       11         55   93.02181           1     cell A 1351.50
#> 16:  cell_95        6         30   59.55714           1     cell A 1228.13
#> 17:  cell_96       10         50   88.31757           1     cell A 1210.65
#> 18: cell_107       16         80  130.62640           1     cell A  969.60
#> 19: cell_113       12         60   99.83100           2     cell B  874.30
#> 20: cell_118       14         70  117.63523           2     cell B  270.00
#>        sdimy        1        2        3
#>  1:  -669.51 3.144429 8.617638 5.853656
#>  2:  -957.71 4.088076 9.410168 4.427447
#>  3:  -950.97 2.899783 9.264667 2.785292
#>  4: -1021.40 4.058155 7.842009 3.405087
#>  5:  -391.16 6.413588 7.374390 2.629099
#>  6:  -668.36 2.989329 9.298030 2.823368
#>  7:  -894.70 7.222222 0.000000 0.000000
#>  8:  -421.27 5.933558 3.031319 2.865092
#>  9:  -669.71 8.067155 0.000000 2.566856
#> 10: -1090.20 2.183105 6.374428 4.449344
#> 11: -1458.00 0.985555 9.382938 1.480231
#> 12: -1829.60 1.715689 8.215992 5.003582
#> 13: -1298.30 0.000000 7.914246 4.373377
#> 14: -1401.00 3.790383 5.580052 8.658080
#> 15: -1923.80 1.839913 9.190628 3.859789
#> 16:  -739.38 2.523159 6.561978 0.000000
#> 17:  -374.81 3.737206 8.241875 1.494778
#> 18: -1198.50 4.579634 8.674903 6.989984
#> 19: -1127.00 5.564253 7.927811 1.291685
#> 20: -1383.30 9.142231 1.263504 6.152727
# visualize total expression information
spatDimCellPlot(mini_giotto_single_cell, cell_annotation_values = 'total_expr')

# visualize enrichment results
spatDimCellPlot(mini_giotto_single_cell,
        spat_enr_names = 'cluster_metagene',
        cell_annotation_values = c('1','2'))