dimCellPlot: dimCellPlot

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

dimCellPlot

Description

Visualize cells according to dimension reduction coordinates

Usage

dimCellPlot(gobject, ...)

Arguments

gobject

giotto object

...

Arguments passed on to dimCellPlot2D spat_unit spatial unit feat_type feature type 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 spat_enr_names names of spatial enrichment results to include cell_annotation_values numeric cell annotation columns 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_code named vector with colors for cell annotation values 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 dim. reduction points point_border_col color of border around points point_border_stroke stroke size of border around points 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 default_save_name default save name for saving, don't change, change save_name in save_param

Details

Description of parameters. For 3D plots see dimCellPlot2D

Value

ggplot

See Also

Other dimension reduction cell annotation visualizations: dimCellPlot2D()

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