subset_feature_plot: Subset feature plot

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Subset feature plot

Description

This function splits the feature plots according to a grouping variable defined in subset.by. The main difference is that the whole dataset is also shown in the background as smaller points.

Usage

subset_feature_plot(
  seu,
  subset.by,
  feature,
  reduction = "umap",
  max.cutoff = "q98",
  min.cutoff = NA,
  slot = "data",
  ncol = NULL,
  col_pal = NULL,
  legend.position = "right",
  pt.size = 2,
  pt.stroke = 0.05,
  pt.shape = 21,
  pt.alpha = 1,
  back.pt.size = 0.5,
  back.pt.alpha = 0.1,
  back.pt.color = "grey",
  combine = TRUE,
  dims_plot = c(1, 2),
  order_points_by_value = TRUE,
  ...
)

Arguments

seu	Seurat object
subset.by	Metadata column whose unique values will generate split feature plots.
feature	Feature to plot.
reduction	Dimensionality reduction to use.
max.cutoff	Maximum cutoff value for feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
min.cutoff	Minimum cutoff value for feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
slot	Slot to extract data from.
ncol	Number of columns for display when having multiple features.
col_pal	Continuous colour palette to use, default "RdYlBu".
legend.position	Position of legend, default "right" (set to "none" for clean plot).
pt.size	Adjust point size for plotting.
pt.stroke	Stroke value for each point.
pt.shape	Adjust point shape for plotting.
pt.alpha	Adjust alpha value for each point.
back.pt.size	Adjust background point size for plotting.
back.pt.alpha	Adjust opacity for background points.
back.pt.color	Colour for background points.
combine	Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects
dims_plot	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions.
order_points_by_value	Logical, should points be ordered by their value (e.g. expression levels), which corresponds to plotting on top cells that have high expression, instead of getting 'buried' by lowly expressed cells.
...	Additional parameters passed to ggplot2::geom_point.

Value

A ggplot2 object.

Author(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.