Make a dotplot of gene expression by cell population
Usage
bb_gene_dotplot(
cds,
markers,
group_cells_by,
reduction_method = "UMAP",
norm_method = c("size_log", "log_only"),
scale_expression_by_gene = FALSE,
lower_threshold = 0,
max.size = 10,
group_ordering = "bicluster",
gene_ordering = NULL,
pseudocount = 1,
scale_max = 3,
scale_min = -3,
colorscale_name = NULL,
sizescale_name = NULL,
...
)Arguments
- cds
A cell data set object
- markers
A character vector of genes to plot
- group_cells_by
A cds colData column. Use "multifactorial" to pick 2 categorical variables to put on X axis and to facet by. See ordering below.
- norm_method
How to normalize gene expression. Size_factor and log normalized or only log normalized.
- scale_expression_by_gene
Whether to scale expression values according to gene. Defaults to FALSE.
- lower_threshold
Lower cutoff for gene expression
- max.size
The maximum size of the dotplot
- group_ordering
Defaults to "biclustering" method from pheatmap. Optionally will take a vector of group values to set the axis order explicitly. If using group_cells_by = "multifactorial" you will need a df to define facet and axis levels. See example.
- gene_ordering
Optional vector of gene names to order the plot.
- pseudocount
Add to zero expressors. Default = 1
- scale_max
Expression scale max
- scale_min
Expression scale min
- colorscale_name
Label for the color scale
- sizescale_name
Label for the size scale
- ...
Additional parameters to pass to facet_wrap.