View source: R/bb_gene_dotplot.R
bb_gene_dotplot | R Documentation |
Make a dotplot of gene expression by cell population
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,
...
)
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. |
A ggplot
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