plotUMAP

plotUMAP

Description

Short wrapper for UMAP visualization

Usage

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

Arguments

Argument	Description
gobject	giotto object
dim_reduction_name	name of UMAP
default_save_name	default save name of UMAP plot
...	Arguments passed on to ``dimPlot2D` <#dimplot2d>`_ list(“n”, ” “, list(list(list(“group_by”)), list(“create multiple plots based on cell annotation column”)), “n”, ” “, list(list(list(“group_by_subset”)), list(“subset the group_by factor column”)), “n”, ” “, list(list(list(“dim1_to_use”)), list(“dimension to use on x-axis”)), “n”, ” “, list(list(list(“dim2_to_use”)), list(“dimension to use on y-axis”)), “n”, ” “, list(list(list(“spat_enr_names”)), list(“names of spatial enrichment results to include”)), “n”, ” “, list(list(

list("show_NN_network")), list("show underlying NN network")), "\n", "    ", list(list(list("nn_network_to_use")), list("type of NN network to use (kNN vs sNN)")), "\n", "    ", list(list(list("network_name")), list("name of NN network to use, if show_NN_network = TRUE")), "\n", "    ", list(list(list("cell_color")), list("color for cells (see details)")), "\n", "    ", list(list(list("color_as_factor")), list("convert color column to factor")), "\n", "    ", list(list(list("cell_color_code")),
list("named vector with colors")), "\n", "    ", list(list(list("cell_color_gradient")), list("vector with 3 colors for numeric data")), "\n", "    ", list(list(list("gradient_midpoint")), list("midpoint for color gradient")), "\n", "    ", list(list(list("gradient_limits")), list("vector with lower and upper limits")), "\n", "    ", list(list(list("select_cell_groups")), list("select subset of cells/clusters based on cell_color parameter")), "\n", "    ", list(list(list("select_cells")), list(
"select subset of cells based on cell IDs")), "\n", "    ", list(list(list("show_other_cells")), list("display not selected cells")), "\n", "    ", list(list(list("other_cell_color")), list("color of not selected cells")), "\n", "    ", list(list(list("other_point_size")), list("size of not selected cells")), "\n", "    ", list(list(list("show_cluster_center")), list("plot center of selected clusters")), "\n", "    ", list(list(list("show_center_label")), list("plot label of selected clusters")),
"\n", "    ", list(list(list("center_point_size")), list("size of center points")), "\n", "    ", list(list(list("center_point_border_col")), list("border color of center points")), "\n", "    ", list(list(list("center_point_border_stroke")), list("border stroke size of center points")), "\n", "    ", list(list(list("label_size")), list("size of labels")), "\n", "    ", list(list(list("label_fontface")), list("font of labels")), "\n", "    ", list(list(list("edge_alpha")), list("column to use for alpha of the edges")),
"\n", "    ", list(list(list("point_shape")), list("point with border or not (border or no_border)")), "\n", "    ", list(list(list("point_size")), list("size of point (cell)")), "\n", "    ", list(list(list("point_alpha")), list("transparancy of point")), "\n", "    ", list(list(list("point_border_col")), list("color of border around points")), "\n", "    ", list(list(list("point_border_stroke")), list("stroke size of border around points")), "\n", "    ", list(list(list("title")), list("title for plot, defaults to cell_color parameter")),
"\n", "    ", list(list(list("show_legend")), list("show legend")), "\n", "    ", list(list(list("legend_text")), list("size of legend text")), "\n", "    ", list(list(list("legend_symbol_size")), list("size of legend symbols")), "\n", "    ", list(list(list("background_color")), list("color of plot background")), "\n", "    ", list(list(list("axis_text")), list("size of axis text")), "\n", "    ", list(list(list("axis_title")), list("size of axis title")), "\n", "    ", list(list(list("cow_n_col")),
    list("cowplot param: how many columns")), "\n", "    ", list(list(list("cow_rel_h")), list("cowplot param: relative height")), "\n", "    ", list(list(list("cow_rel_w")), list("cowplot param: relative width")), "\n", "    ", list(list(list("cow_align")), list("cowplot param: how to align")), "\n", "    ", list(list(list("show_plot")), list("show plot")), "\n", "    ", list(list(list("return_plot")), list("return ggplot object")), "\n", "    ", list(list(list("save_plot")), list("directly save the plot [boolean]")),
"\n", "    ", list(list(list("save_param")), list("list of saving parameters, see ", list(list("showSaveParameters")))), "\n", "  ")

Details

Description of parameters, see ``dimPlot2D` <#dimplot2d>`_ . For 3D plots see ``plotUMAP_3D` <#plotumap3d>`_

Value

ggplot

Seealso

Other reduced dimension visualizations:

``dimPlot2D` <#dimplot2d>`_ , ``dimPlot3D` <#dimplot3d>`_ , ``dimPlot` <#dimplot>`_ , ``plotPCA_2D` <#plotpca2d>`_ , ``plotPCA_3D` <#plotpca3d>`_ , ``plotPCA` <#plotpca>`_ , ``plotTSNE_2D` <#plottsne2d>`_ , ``plotTSNE_3D` <#plottsne3d>`_ , ``plotTSNE` <#plottsne>`_ , ``plotUMAP_2D` <#plotumap2d>`_ , ``plotUMAP_3D` <#plotumap3d>`_

Examples

data(mini_giotto_single_cell)

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