Plots expression for one or more genes as a function of pseudotime
plot_genes_in_pseudotime(
cds_subset,
min_expr = NULL,
cell_size = 0.75,
nrow = NULL,
ncol = 1,
panel_order = NULL,
color_cells_by = "pseudotime",
trend_formula = "~ splines::ns(pseudotime, df=3)",
label_by_short_name = TRUE,
vertical_jitter = NULL,
horizontal_jitter = NULL
)subset cell_data_set including only the genes to be plotted.
the minimum (untransformed) expression level to plot.
the size (in points) of each cell used in the plot.
the number of rows used when laying out the panels for each gene's expression.
the number of columns used when laying out the panels for each gene's expression
vector of gene names indicating the order in which genes
should be laid out (left-to-right, top-to-bottom). If
label_by_short_name = TRUE, use gene_short_name values, otherwise
use feature IDs.
the cell attribute (e.g. the column of colData(cds)) to be used to color each cell.
the model formula to be used for fitting the expression trend over pseudotime.
label figure panels by gene_short_name (TRUE) or feature ID (FALSE).
A value passed to ggplot to jitter the points in the vertical dimension. Prevents overplotting, and is particularly helpful for rounded transcript count data.
A value passed to ggplot to jitter the points in the horizontal dimension. Prevents overplotting, and is particularly helpful for rounded transcript count data.
a ggplot2 plot object