dimred_qc_plots: QC and general metadata plots visualised on dimensional...

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

QC and general metadata plots visualised on dimensional reduced space

Description

This function generates QC and general metadata plots that are visualised in dimensional reduced space (e.g. PCA and UMAP). The aim is to visualise weather there are any technical factors driving the variability in the data, e.g. integration driven by sample, correlation of specific PCs with number of genes expressed in a cell, etc.

Usage

dimred_qc_plots(
  seu,
  reductions = c("pca"),
  metadata_to_plot = NULL,
  qc_to_plot = NULL,
  plot_dir,
  max.cutoff = "q98",
  min.cutoff = NA,
  legend.position = "right",
  cont_col_pal = NULL,
  discrete_col_pal = NULL,
  dims_plot = c(1, 2),
  pt.size = 1.4,
  fig.res = 200,
  ...
)

Arguments

seu	Seurat object (required).
reductions	Vector with dimensional reductions objects to use for plotting the metadata and QC features.
metadata_to_plot	Vector with metadata names to plot, they should be present in the meta.data slot.
qc_to_plot	Vector with QC names to plot, they should be present in the meta.data slot.
plot_dir	Directory to save generated plots. If NULL, plots are not saved.
max.cutoff	Vector of maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
min.cutoff	Vector of minimum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
legend.position	Position of legend, default "right" (set to "none" for clean plot).
cont_col_pal	Continuous colour palette to use, default "RdYlBu".
discrete_col_pal	Discrete colour palette to use, default is Hue palette (hue_pal) from 'scales' package.
dims_plot	Dimensions to plot. For UMAP and TSNE this is set to c(1,2).
pt.size	Adjust point size for plotting.
fig.res	Figure resolution in ppi (see 'png' function).
...	Additional named parameters passed to Seurat's DimPlot and FeaturePlot.

Value

Nothing, plots are saved in the specified folder if not NULL.

Author(s)

C.A.Kapourani [e-mail]

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