PreparePlotData

Prepares a tidy data frame of pathway activity scores per cell for downstream plotting with PlotPathway() or CalculatePercentage(). Accepts either a plain metadata data frame or a Seurat object.

Usage

PreparePlotData(x, score, group, Seurat.object = FALSE)

Arguments

x

A metadata data frame (rows = cells, columns = metadata fields) or a Seurat object. Must contain the column specified by group.

score

A named numeric vector of per-cell scores from ComputeCellData(). Names must be cell IDs matching rownames of x.

group

A character string giving the column name in x metadata to use for grouping (e.g. "genotype", "Age").

Seurat.object

Logical; set TRUE if x is a Seurat object. Default FALSE.

Value

A data frame with one row per cell and three columns:

normalized

Normalized pathway activity score in [0, 1]\ from ComputeCellData().

scale

Z-scored pathway activity across all cells.

The grouping variable, named after the group argument.

Examples

if (FALSE) { # \dontrun{
# Using a plain metadata data frame
plotdata <- PreparePlotData(metadata_df, scores, "genotype")

# Using a Seurat object
plotdata <- PreparePlotData(seurat_obj, scores, "orig.ident", Seurat.object = TRUE)
} # }