Make a plot of gene expression in UMAP form
Usage
bb_gene_violinplot(
cds,
variable,
genes_to_plot,
experiment_type = "Gene Expression",
pseudocount = 1,
include_jitter = FALSE,
ytitle = "Expression",
plot_title = NULL,
rows = 1,
show_x_label = TRUE,
legend_pos = "none",
comparison_list = NULL,
palette = NULL,
violin_alpha = 1,
jitter_alpha = 1,
jitter_color = "black",
jitter_fill = "transparent",
jitter_size = 0.5,
facet_scales = "fixed",
order_genes = TRUE,
jitter_match = FALSE,
rasterize = FALSE,
raster_dpi = 300
)Arguments
- cds
A cell data set object
- variable
Stratification variable for x-axis
- genes_to_plot
Either a character vector of gene short names or a tbl/df where the first column is gene short name and the second is the gene grouping.
- pseudocount
Value to add to zero-cells
- include_jitter
Include jitter points
- ytitle
Title for y axis
- plot_title
Main title for the plot
- rows
Number of rows for facetting
- show_x_label
Option to show x label
- legend_pos
Position for label
- comparison_list
Optional list of comparisons for ggpubr
- palette
Color palette to use. Viridis is default.
- violin_alpha
Alpha value for violin plot
- jitter_alpha
Alpha value for jitter plot
- jitter_color
Color for the jitter plot. Defaults to black and ignored if jitter_match == TRUE
- jitter_fill
Fill for the jitter plot
- jitter_size
Size of the jitter points
- facet_scales
Scale option for facetting. "Fixed" is default
- order_genes
If true, put genes in the same order as variable parameter
- jitter_match
If true, match jitter color to violin fill.
- rasterize
Whether to render the graphical layer as a raster image. Default is FALSE.
- raster_dpi
If rasterize then this is the DPI used. Default = 300.