PSIPlot

Source code

Description

Plot PSI score on reduction map.

Usage

PSIPlot(
  object = NULL,
  exon.assay = NULL,
  exclude.assay = "exclude",
  features = NULL,
  dims = c(1, 2),
  cells = NULL,
  cols = c("lightgrey", "red"),
  pt.size = NULL,
  alpha = 1,
  order = TRUE,
  reduction = NULL,
  shape.by = NULL,
  ncol = NULL,
  split.by = NULL,
  by.col = TRUE,
  coord.fixed = FALSE,
  combine = TRUE,
  raster = NULL,
  raster.dpi = c(512, 512)
)

Arguments

object Seurat object.
exon.assay Exon assay name.
exclude.assay Excluded exon assay name.
features Features to plot.
dims Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
cells Vector of cells to plot (default is all cells)
cols Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by RColorBrewer::brewer.pal.info.
pt.size Adjust point size for plotting
alpha Alpha value for points
order Boolean determing whether to plot cells in order of PSI score.
reduction Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
shape.by If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells. Only applicable if raster = FALSE.
ncol Number of columns to combine multiple features plots to
split.by A factor in object metadata to split the plot by, pass ‘ident’ to split by cell identity
by.col If splitting by a factor, plot the splits per column with the features as rows
coord.fixed Plot cartesian coordinates with fixed aspect ratio
combine Combine plots into a single patchwork ggplot object. If FALSE, return a list of ggplot objects.
raster.dpi Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
min.cutoff, max.cutoff Vector of minimum and maximum cutoff values for each feature
mode Test mode. For mode 1, X (test feature) vs Y (binding feature). For mode 2, X vs (Y-X). For mode 3, X vs (Y+X). Please note, when set to mode 2 or 3, will use raw counts to update expression value of binding features. Then normalise the counts before testing. For mode 1, will use Layer ‘data’. Default is mode 1.
group.by Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass ‘ident’ to group by identity class

Value

A patchwork ggplot object of combine = TRUE; otherwise, a list of ggplot objects

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