dimPlot: dimPlot

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

dimPlot

Description

Visualize cells according to dimension reduction coordinates

Usage

dimPlot(...)

Arguments

...

Arguments passed on to dimPlot2D gobject giotto object group_by create multiple plots based on cell annotation column group_by_subset subset the group_by factor column 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 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 default_save_name default save name for saving, don't change, change save_name in save_param

Details

Description of parameters, see dimPlot2D. For 3D plots see dimPlot3D

Value

ggplot

See Also

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

Examples

data(mini_giotto_single_cell)

dimPlot(mini_giotto_single_cell)
dimPlot(mini_giotto_single_cell, cell_color = 'cell_types', point_size = 3)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.