Visualize features between the query and reference Seurat objects by RunSeuratMap2Ref()

Visualize features between the query and reference Seurat objects by RunSeuratMap2Ref()

Usage

VizSeuratMap2Ref(
  query,
  ref,
  features,
  split_by = NULL,
  plot_type = c("dim", "violin", "box", "bar", "ridge", "heatmap", "dot"),
  reduction = NULL,
  ident = NULL,
  combine = TRUE,
  nrow = NULL,
  ncol = ifelse(length(features) > 1, 1, 2),
  byrow = NULL,
  axes = NULL,
  axis_titles = NULL,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

query

A Seurat object with query data

ref

A Seurat object with reference data

features

Features from the query and reference to visualize. The format is 'query:ref' or 'feature', where 'feature' is the same in both query and reference. The query and reference features must be the same type (numeric or factor/character). All features must be in the same type. A special case is to visualize the mapping score, for example "seurat_clusters.score". If so, only one feature can be provided, and the plot type must be "dim". The reference will be plotted with the identity of the reference dataset.

split_by

Column name in the query object to split the plot by, will not be supported. The plot will be split by the query/reference features instead.

plot_type

Type of plot to generate. One of 'dim', 'violin', 'box', 'bar', 'ridge', 'heatmap' and 'dot'.

'dim': Dimensionality reduction plot. If the features are numeric, scplotter::FeatureStatPlot() will be used. If the features are factor/character, scplotter::CellDimPlot() will be used.
other: scplotter::FeatureStatPlot() will be used.

reduction

Dimensionality reduction to use for the plot. If NULL, the default reduction will be used for both query and reference. If the format is 'reduction_q:reduction_r', the first part will be used for the query and the second part for the reference. If the format is 'reduction', the same reduction will be used for both query and reference.

ident

Column name in the query and reference object to use for the plot. If NULL, the default identity will be used for both query and reference. If the format is 'ident_q:ident_r', the first part will be used for the query and the second part for the reference. If the format is 'ident', the same identity will be used for both query and reference.

combine

Whether to combine the plots into one plot. If FALSE, the plots will be returned as a list.

nrow

Number of rows to use for the combined plot. If NULL, the number of rows will be calculated based on the number of features and ncol. If ncol is NULL, the number of columns will be calculated based on the number of features and nrow.

ncol

Number of columns to use for the combined plot. If NULL, the number of columns will be calculated based on the number of features and nrow. If nrow is NULL, the number of rows will be calculated based on the number of features and ncol.

byrow

Whether to combine the plots by row or column.

axes

Whether to show the axes for the combined plot.

axis_titles

Whether to show the axis titles for the combined plot.

guides

Whether to show the guides for the combined plot.

design

Design for the combined plot. See also patchwork::wrap_plots().

...

Additional arguments to pass to the plot function