`dimGenePlot`¶

dimGenePlot

Description¶

Visualize gene expression according to dimension reduction coordinates

Usage¶

dimGenePlot(...)

Arguments¶

Argument

Description

...

Arguments passed on to ``dimGenePlot2D` <#dimgeneplot2d>`_ list(“n”, ” “, list(list(list(“gobject”)), list(“giotto object”)), “n”, ” “, list(list(list(“expression_values”)), list(“gene expression values to use”)), “n”, ” “, list(list(list(“genes”)), list(“genes to show”)), “n”, ” “, list(list(list(“dim_reduction_to_use”)), list(“dimension reduction to use”)), “n”, ” “, list(list(list(“dim_reduction_name”)), list(“dimension reduction name”)), “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("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("network_color")), list("color of NN network")), "\n", "    ", list(list(list("edge_alpha")), list("column to use for alpha of the edges")),
"\n", "    ", list(list(list("scale_alpha_with_expression")), list("scale expression with ggplot alpha parameter")), "\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 points")), "\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("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("show_legend")), list("show legend")), "\n", "    ", list(list(list("legend_text")), list("size of legend text")),
"\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 plots")), "\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", "    ", list(list(list("default_save_name")), list("default save name for saving, don't change, change save_name in save_param")),
"\n", "  ")

Details¶

Description of parameters.

Value¶

ggplot

Seealso¶

``dimGenePlot3D` <#dimgeneplot3d>`_

Other dimension reduction gene expression visualizations: ``dimGenePlot2D` <#dimgeneplot2d>`_ , ``dimGenePlot3D` <#dimgeneplot3d>`_

Examples¶

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
dimGenePlot(mini_giotto_single_cell, genes = selected_genes, point_size = 3)

dimGenePlot¶