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SEM Graph with t test on cluster level

Source: R/plotting_functions.R
DO.BarplotClustert.Rd

Perform SEM-based graphs with t-test on cluster level for Seurat objects. Calculates mean expression values and SEM for selected features, and visualizes them. Performs pairwise t-tests comparing conditions, with optional custom control condition and clustering. Optionally returns a summary data frame.

Usage

DO.BarplotClustert(
  sce_object,
  Feature,
  ListTest = NULL,
  returnValues = FALSE,
  ctrl.condition = NULL,
  group.by = "condition",
  returnPlot = TRUE,
  bar_colours = NULL,
  stat_pos_mod = 1.15,
  step_mod = 0.2,
  x_label_rotation = 45,
  y_limits = NULL,
  log1p_nUMI = TRUE
)

Arguments

sce_object

Combined SCE object or Seurat

Feature

gene name

ListTest

List for which conditions t-test will be performed, if NULL always against provided CTRL

returnValues

return df.melt.sum data frame containing means and SEM for the set group

ctrl.condition

set your ctrl condition, relevant if running with empty comparison List

group.by

select the seurat object slot where your conditions can be found, default conditon

returnPlot

IF TRUE returns ggplot

bar_colours

colour vector

stat_pos_mod

Defines the distance to the graphs of the statistic

step_mod

Defines the distance between each statistics bracket

x_label_rotation

Rotation of x-labels

y_limits

set limits for y-axis

log1p_nUMI

If nUMIs should be log1p transformed

Value

a ggplot or a dataframe

Author

Mariano Ruz Jurado

Examples

sce_data <- readRDS(system.file("extdata", "sce_data.rds", package = "DOtools"))

set.seed(123)
sce_data$orig.ident <- sample(rep(c("A", "B", "C"), length.out = ncol(sce_data)))

ListTest <- list()
ListTest[[1]] <- c("healthy", "disease")


DO.BarplotClustert(
  sce_object = sce_data,
  Feature = "NKG7",
  ListTest = ListTest,
  ctrl.condition = "healthy",
  group.by="condition"
)
#> Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
#> ℹ Please use `rlang::check_installed()` instead.
#> ℹ The deprecated feature was likely used in the Seurat package.
#>   Please report the issue at <https://github.com/satijalab/seurat/issues>.
#> Warning: The `slot` argument of `SetAssayData()` is deprecated as of SeuratObject 5.0.0.
#> ℹ Please use the `layer` argument instead.
#> ℹ The deprecated feature was likely used in the Seurat package.
#>   Please report the issue at <https://github.com/satijalab/seurat/issues>.
#> Using condition, orig.ident as id variables