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Run Monocle2 analysis

Source: R/RunMonocle.R
RunMonocle2.Rd

Run Monocle2 analysis

Usage

RunMonocle2(
  srt,
  assay = NULL,
  layer = "counts",
  group.by = NULL,
  expressionFamily = "negbinomial.size",
  features = NULL,
  feature_type = "HVF",
  disp_filter = "mean_expression >= 0.1 & dispersion_empirical >= 1 * dispersion_fit",
  max_components = 2,
  reduction_method = "DDRTree",
  norm_method = "log",
  residualModelFormulaStr = NULL,
  pseudo_expr = 1,
  root_state = NULL,
  seed = 11,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used.

layer

Which layer to use. Default is "counts".

group.by

Name of one or more meta.data columns to group (color) cells by.

expressionFamily

The distribution family to use for modeling gene expression. Default is "negbinomial.size".

features

A character vector of features to use. Defaults to NULL, in which case features were determined by feature_type.

feature_type

The type of features to use in the analysis. Possible values are "HVF" for highly variable features or "Disp" for features selected based on dispersion. Default is "HVF".

disp_filter

A string specifying the filter to use when feature_type is "Disp". Default is "mean_expression >= 0.1 & dispersion_empirical >= 1 * dispersion_fit".

max_components

The maximum number of dimensions to use for dimensionality reduction. Default is 2.

reduction_method

The dimensionality reduction method to use. Possible values are "DDRTree", "ICA", "tSNE", "SimplePPT", "L1-graph", "SGL-tree". Default is "DDRTree".

norm_method

The normalization method to use. Possible values are "log" and "none". Default is "log".

residualModelFormulaStr

A model formula specifying the effects to subtract. Default is NULL.

pseudo_expr

Amount to increase expression values before dimensionality reduction. Default is 1.

root_state

The state to use as the root of the trajectory. If NULL, will prompt for user input.

seed

Random seed for reproducibility. Default is 11.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object with the Monocle2 analysis results added to the @tools slot.

See also

RunSlingshot, CellDimPlot, FeatureDimPlot

Examples

if (interactive()) {
  data(pancreas_sub)
  pancreas_sub <- standard_scop(pancreas_sub)
  pancreas_sub <- RunMonocle2(
    pancreas_sub,
    group.by = "SubCellType"
  )
  names(pancreas_sub@tools$Monocle2)
  trajectory <- pancreas_sub@tools$Monocle2$trajectory

  p1 <- CellDimPlot(
    pancreas_sub,
    group.by = "Monocle2_State",
    reduction = "DDRTree",
    label = TRUE,
    theme_use = "theme_blank"
  )
  p1

  p1 + trajectory

  FeatureDimPlot(
    pancreas_sub,
    features = "Monocle2_Pseudotime",
    reduction = "UMAP",
    theme_use = "theme_blank"
  )

  pancreas_sub <- RunMonocle2(
    pancreas_sub,
    feature_type = "Disp",
    disp_filter = "mean_expression >= 0.01 & dispersion_empirical >= 1 * dispersion_fit"
  )
  trajectory <- pancreas_sub@tools$Monocle2$trajectory
  p2 <- CellDimPlot(
    pancreas_sub,
    group.by = "Monocle2_State",
    reduction = "DDRTree",
    label = TRUE,
    theme_use = "theme_blank"
  )
  p2

  p2 + trajectory

  FeatureDimPlot(
    pancreas_sub,
    features = "Monocle2_Pseudotime",
    reduction = "UMAP",
    theme_use = "theme_blank"
  )
}