boxplot.cell.clustering: Boxplots for identified clusters

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Boxplots for identified clusters

Description

It draws a boxplot with cell clusters identified through FlowCT::fsom.clustering().

Usage

boxplot.cell.clustering(
  fcs.SCE,
  assay.i = "normalized",
  cell.clusters,
  condition = "condition",
  return.mode = "percentage",
  log.trans = FALSE,
  color.by = condition,
  facet = FALSE,
  facet.free.scale = "free_x",
  y.limits,
  return.stats = FALSE,
  plot.only.sig = c(F, 0.05),
  cond.colors,
  color.by.colors
)

Arguments

fcs.SCE	A fcs.SCE object generated through FlowCT::fcs.SCE().
assay.i	Name of matrix stored in the fcs.SCE object from which calculate correlation. Default = "normalized".
cell.clusters	Name of column containing clusters identified through FlowCT::clustering.flow().
condition	Column name from the colData(fcs.SCE) object which contains condition information.
return.mode	String for specifying if final resuls should be proportions ("percentage") or raw counts ("counts"). Default = "percentage".
log.trans	Logarithmic transformation of counts/percentage values?. Default = FALSE.
color.by	Variable name (from colData(fcs.SCE)) for lines coloring. Default, same as condition.
facet	Logical indicating if splitting boxplots by cell clusters. Default = FALSE.
facet.free.scale	If facet = TRUE, string indicating how scales would be shared across all facets. Possible values: "free_x" (default), "free_y" and "free".
shape.by	Variable name (from colData(fcs.SCE)) for dot shaping. Default = NULL.
y.limits	Numeric vector with limits for y-axis (minimum, maximum).
return.stats	Logical indicating if calculated statistics should be returned in a new variable. Default = FALSE.
plot.only.sig	Vector indicating if only significant cell clusters should be displayed (logical element) and the P-value cutoff for selecting those ones (numerical element). Default = c(FALSE, 0.05).
cond.colors	Vector with colors for plotting option condition.
color.by.colors	Vector with colors for plotting option color.by.

Examples

## Not run: 
# option 1: show all cell clusters and return statistics
bx_sig <- boxplot.cell.clustering(fcs.SCE = fcs, cell.clusters = "SOM_named", facet = T,
    facet.free.scale = "free", return.stats = T)

# option 2: show only those significant cell clusters
boxplot.cell.clustering(fcs.SCE = fcs, cell.clusters = "SOM_named",
    plot.only.sig = c(T, 0.1))

## End(Not run)

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.