Creates a scatter plot of two features (typically feature expression), across a set of single cells. Cells are colored by their identity class. Pearson correlation between the two features is displayed above the plot.
FeatureScatter( object, feature1, feature2, cells = NULL, shuffle = FALSE, seed = 1, group.by = NULL, cols = NULL, pt.size = 1, shape.by = NULL, span = NULL, smooth = FALSE, combine = TRUE, slot = "data", plot.cor = TRUE, raster = NULL, jitter = TRUE )
First feature to plot. Typically feature expression but can also be metrics, PC scores, etc. - anything that can be retreived with FetchData
Second feature to plot.
Cells to include on the scatter plot.
Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (default is FALSE)
Sets the seed if randomly shuffling the order of points.
Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
Colors to use for identity class plotting.
Size of the points on the plot
Ignored for now
Spline span in loess function call, if
Smooth the graph (similar to smoothScatter)
Combine plots into a single
Slot to pull data from, should be one of 'counts', 'data', or 'scale.data'
Display correlation in plot title
Convert points to raster format, default is
Jitter for easier visualization of crowded points
A ggplot object
data("pbmc_small") FeatureScatter(object = pbmc_small, feature1 = 'CD9', feature2 = 'CD3E')