Short wrapper for UMAP visualization
plotUMAP_2D(
gobject,
dim_reduction_name = "umap",
default_save_name = "UMAP_2D",
...
)
giotto object
name of UMAP
default save name of UMAP plot
Arguments passed on to dimPlot2D
group_by
create multiple plots based on cell annotation column
group_by_subset
subset the group_by factor column
dim1_to_use
dimension to use on x-axis
dim2_to_use
dimension to use on y-axis
spat_enr_names
names of spatial enrichment results to include
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
cell_color
color for cells (see details)
color_as_factor
convert color column to factor
cell_color_code
named vector with colors
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
show_other_cells
display not selected cells
other_cell_color
color of not selected cells
other_point_size
size of not selected cells
show_cluster_center
plot center of selected clusters
show_center_label
plot label of selected clusters
center_point_size
size of center points
center_point_border_col
border color of center points
center_point_border_stroke
border stroke size of center points
label_size
size of labels
label_fontface
font of labels
edge_alpha
column to use for alpha of the edges
point_shape
point with border or not (border or no_border)
point_size
size of point (cell)
point_alpha
transparancy of point
point_border_col
color of border around points
point_border_stroke
stroke size of border around points
title
title for plot, defaults to cell_color parameter
show_legend
show legend
legend_text
size of legend text
legend_symbol_size
size of legend symbols
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 plot
return_plot
return ggplot object
save_plot
directly save the plot [boolean]
save_param
list of saving parameters, see showSaveParameters
ggplot
Description of parameters, see dimPlot2D
. For 3D plots see plotUMAP_3D
Other reduced dimension visualizations:
dimPlot2D()
,
dimPlot3D()
,
dimPlot()
,
plotPCA_2D()
,
plotPCA_3D()
,
plotPCA()
,
plotTSNE_2D()
,
plotTSNE_3D()
,
plotTSNE()
,
plotUMAP_3D()
,
plotUMAP()
data(mini_giotto_single_cell)
plotUMAP_2D(mini_giotto_single_cell)
plotUMAP_2D(mini_giotto_single_cell, cell_color = 'cell_types', point_size = 3)