module_score_analysis: Module score analysis

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Module score analysis

Description

This function takes a group of modules and calculates module scores for the expression programs. In addition, if plot_dir is not NULL creates feature plots with marker genes and the module score and saved them in plot_dir directory.

Usage

module_score_analysis(
  seu,
  modules_group,
  plot_dir = NULL,
  reduction = "umap",
  max.cutoff = "q98",
  min.cutoff = NA,
  legend.position = "top",
  col_pal = NULL,
  dims_plot = c(1, 2),
  seed = 1,
  pt.size = 1.4,
  fig.res = 200,
  alpha = c(0.1, 0.9),
  pt.size.factor = 1.1,
  spatial_col_pal = "inferno",
  crop = FALSE,
  plot_spatial_markers = FALSE,
  spatial_legend_position = "top",
  ...
)

Arguments

seu	Seurat object (required).
modules_group	Group of modules (named list of lists) storing features (e.g. genes) to compute module score for each identified cluster. This step can be useful for annotating the different clusters by saving dot plots for each group. Assumes that we already have computed the modules e.g. by calling the 'module_score_analysis' function. If 'plot_dir' is NULL, no plots will be generated.
plot_dir	Directory to save generated plots. If NULL, plots are not saved.
reduction	Which dimensionality reduction to use (required).
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).
col_pal	Continuous colour palette to use, default "RdYlBu".
dims_plot	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions.
seed	Set a random seed, for reproducibility.
pt.size	Adjust point size for plotting.
fig.res	Figure resolution in ppi (see 'png' function).
alpha	(Spatial) Controls opacity of spots. Provide as a vector specifying the min and max range of values (between 0 and 1).
pt.size.factor	(Spatial) Scale the size of the spots.
spatial_col_pal	(Spatial) Continuous colour palette to use from viridis package to colour spots on tissue, default "inferno".
crop	(Spatial) Crop the plot in to focus on spots that passed QC. Set to FALSE to show entire background image.
plot_spatial_markers	(Spatial) Logical, whether to create spatial feature plots with expression of individual genes.
spatial_legend_position	(Spatial) Position of legend for spatial plots, default "top" (set to "none" for clean plot).
...	Additional named parameters passed to Seurat's AddModuleScore and FeaturePlot

Value

Updated Seurat object with calculated module scores in metadata.

Author(s)

C.A.Kapourani [e-mail]

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