Plot dimension reduction 2D#
Last Updated: Sep 07, 2023
Description#
Visualize cells according to dimension reduction coordinates
Usage#
dimPlot2D(
gobject,
spat_unit = NULL,
feat_type = NULL,
group_by = NULL,
group_by_subset = NULL,
dim_reduction_to_use = "umap",
dim_reduction_name = NULL,
dim1_to_use = 1,
dim2_to_use = 2,
spat_enr_names = NULL,
show_NN_network = FALSE,
nn_network_to_use = "sNN",
network_name = "sNN.pca",
cell_color = NULL,
color_as_factor = TRUE,
cell_color_code = NULL,
cell_color_gradient = c("blue", "white", "red"),
gradient_midpoint = NULL,
gradient_limits = NULL,
select_cell_groups = NULL,
select_cells = NULL,
show_other_cells = TRUE,
other_cell_color = "lightgrey",
other_point_size = 0.5,
show_cluster_center = FALSE,
show_center_label = TRUE,
center_point_size = 4,
center_point_border_col = "black",
center_point_border_stroke = 0.1,
label_size = 4,
label_fontface = "bold",
edge_alpha = NULL,
point_shape = c("border", "no_border"),
point_size = 1,
point_alpha = 1,
point_border_col = "black",
point_border_stroke = 0.1,
title = NULL,
show_legend = TRUE,
legend_text = 10,
legend_symbol_size = 2,
background_color = "white",
axis_text = 8,
axis_title = 8,
cow_n_col = NULL,
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 = "dimPlot2D"
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
create multiple plots based on cell annotation column |
|
subset the group_by factor column |
|
dimension reduction to use |
|
dimension reduction name |
|
dimension to use on x-axis |
|
dimension to use on y-axis |
|
names of spatial enrichment results to include |
|
show underlying NN network |
|
type of NN network to use (kNN vs sNN) |
|
name of NN network to use, if show_NN_network = TRUE |
|
color for cells (see details) |
|
convert color column to factor |
|
named vector with colors |
|
vector with 3 colors for numeric data |
|
midpoint for color gradient |
|
vector with lower and upper limits |
|
select subset of cells/clusters based on cell_color parameter |
|
select subset of cells based on cell IDs |
|
display not selected cells |
|
color of not selected cells |
|
size of not selected cells |
|
plot center of selected clusters |
|
plot label of selected clusters |
|
size of center points |
|
border color of center points |
|
border stroke size of center points |
|
size of labels |
|
font of labels |
|
column to use for alpha of the edges |
|
point with border or not (border or no_border) |
|
size of point (cell) |
|
transparancy of point |
|
color of border around points |
|
stroke size of border around points |
|
title for plot, defaults to cell_color parameter |
|
show legend |
|
size of legend text |
|
size of legend symbols |
|
color of plot background |
|
size of axis text |
|
size of axis title |
|
cowplot param: how many columns |
|
cowplot param: relative heights of rows (e.g. c(1,2)) |
|
cowplot param: relative widths of columns (e.g. c(1,2)) |
|
cowplot param: how to align |
|
show plot |
|
return ggplot object |
|
directly save the plot [boolean] |
|
list of saving parameters, see
|
|
default save name for saving, don’t change, change save_name in save_param |
Details#
Description of parameters. For 3D plots see dimPlot3D
Value#
ggplot
See Also#
Other reduced dimension visualizations: dimPlot3D()
, dimPlot()
,
plotPCA_2D()
, plotPCA_3D()
, plotPCA()
, plotTSNE_2D()
,
plotTSNE_3D()
, plotTSNE()
, plotUMAP_2D()
, plotUMAP_3D()
,
plotUMAP()