Create a dot plot to visualize the mean gene expression and percentage of expressed cells in each group of cells
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
)A cell_data_set for plotting.
A list of gene ids (or short names) to show in the plot
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.
The dimensionality reduction method used for clusters and partitions.
Determines how to transform expression values prior to plotting. Options are "log" and "size_only". Default is "log".
The lowest gene expressed treated as expressed. By default, zero.
The maximum size of the dot. By default, it is 10.
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'.
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".
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).
A pseudo-count added to the average gene expression.
The maximum value (in standard deviations) to show in the heatmap. Values larger than this are set to the max.
The minimum value (in standard deviations) to show in the heatmap. Values smaller than this are set to the min.
a ggplot2 plot object