plot_genes_by_group: Create a dot plot to visualize the mean gene expression and...

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Create a dot plot to visualize the mean gene expression and percentage of expressed cells in each group of cells

Description

Create a dot plot to visualize the mean gene expression and percentage of expressed cells in each group of cells

Usage

plot_genes_by_group(
  cds,
  markers,
  group_cells_by = "cluster",
  reduction_method = "UMAP",
  norm_method = c("log", "size_only"),
  lower_threshold = 0,
  max.size = 10,
  ordering_type = c("cluster_row_col", "maximal_on_diag", "none"),
  axis_order = c("group_marker", "marker_group"),
  flip_percentage_mean = FALSE,
  pseudocount = 1,
  scale_max = 3,
  scale_min = -3,
  color_by_group = FALSE
)

Arguments

cds	A cell_data_set for plotting.
markers	A list of gene ids (or short names) to show in the plot
group_cells_by	How to group cells when labeling them. Must be either the name of a column of colData(cds), or one of "clusters" or "partitions". If a column in colData(cds), must be a categorical variable.
reduction_method	The dimensionality reduction method used for clusters and partitions.
norm_method	Determines how to transform expression values prior to plotting. Options are "log" and "size_only". Default is "log".
lower_threshold	The lowest gene expressed treated as expressed. By default, zero.
max.size	The maximum size of the dot. By default, it is 10.
ordering_type	How to order the genes / groups on the dot plot. Only accepts 'cluster_row_col' (use biclustering to cluster the rows and columns), 'maximal_on_diag' (position each column so that the maximal color shown on each column on the diagonal, if the current maximal is used in earlier columns, the next largest one is position), and 'none' (preserve the ordering from the input gene or alphabetical ordering of groups). Default is 'cluster_row_col'.
axis_order	Whether to put groups on x-axis, genes on y-axis (option 'group_marker') or the reverse order (option 'marker_group'). Default is "group_marker".
flip_percentage_mean	Logical indicating whether to use color of the dot to represent the percentage (by setting flip_percentage_mean = FALSE, default) and size of the dot the mean expression, or the opposite (by setting flip_percentage_mean = TRUE).
pseudocount	A pseudo-count added to the average gene expression.
scale_max	The maximum value (in standard deviations) to show in the heatmap. Values larger than this are set to the max.
scale_min	The minimum value (in standard deviations) to show in the heatmap. Values smaller than this are set to the min.
color_by_group	Color cells by the group to which they belong.

Value

a ggplot2 plot object

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.