plotUMAP: plotUMAP

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plotUMAP

Description

Short wrapper for UMAP visualization

Usage

plotUMAP(gobject, dim_reduction_name = NULL, default_save_name = "UMAP", ...)

Arguments

gobject	giotto object
dim_reduction_name	name of UMAP
default_save_name	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 spat_unit spatial unit (e.g. "cell") feat_type feature type (e.g. "rna", "dna", "protein") 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 for not selected cells other_point_size point size for 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 transparency of points 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 heights of rows (e.g. c(1,2)) cow_rel_w cowplot param: relative widths of columns (e.g. c(1,2)) 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

Details

Description of parameters, see dimPlot2D. For 3D plots see plotUMAP_3D

Value

ggplot

See Also

Other reduced dimension visualizations: dimPlot2D(), dimPlot3D(), dimPlot(), plotPCA_2D(), plotPCA_3D(), plotPCA(), plotTSNE_2D(), plotTSNE_3D(), plotTSNE(), plotUMAP_2D(), plotUMAP_3D()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.