MakeEnrichmentDotPlot: MakeEnrichmentDotPlot

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

MakeEnrichmentDotPlot

Description

An extremely overloaded function that calculates statistics and enrichment in Seurat Objects. Please see an example dot plot before using this function. Note the aggregated data can be obtained from the ggplot object (i.e. P1$data)

Usage

MakeEnrichmentDotPlot(
  seuratObj,
  yField = "ClusterNames_0.2",
  xField = "Timepoint",
  colorField = "Tissue",
  colorLabels = NULL,
  extraGroupingFields = NULL,
  normalizationField = "cDNA_ID",
  sizeFactorField = "SizeFactor",
  maxSizeFactor = 100,
  independentVariableTestField = colorField,
  dependentVariableTestField = sizeFactorField
)

Arguments

seuratObj	The seurat object that holds the data.
yField	The y axis for the dotplots.
xField	The x axis for the dotplots.
colorField	The column of metadata that is used for the colorField. This should be a factor with two levels. The highest level, reported by levels(), will be treated as the 'highest' value.
colorLabels	Vector of length 2-3 that defines the extremes and midpoint of the colorField axis. If null, the values of colorField will be used.
extraGroupingFields	An optional vector of additional fields to use in grouping
normalizationField	The metadata column that is used for size factor calculation (equivalently, normalization between different datasets.) Recommended to be cDNA_ID.
sizeFactorField	The column name of the seruat object metadata that size factors should be stored in.
maxSizeFactor	The maximum allowable SizeFactor before an error is automatically thrown. For instance, a size factor of 100 means you have a group of 8000 cells that you're comparing to 80 cells.
independentVariableTestField	This and dependentVariableTestField automatically define a small statistical test to see if your size factors are correlated. Ideally, they should not be if independentVariableTestField is not the same value as normalizationField.
dependentVariableTestField	This value should be equal to sizeFactorField initially, but can be changed to interactively see other correlations in the metadata.

bimberlabinternal/CellMembrane documentation built on Nov. 15, 2024, 9:34 p.m.