Generate a boxplot of MFI (median fluorescence intensity) for each cluster identified by TockyKmeans. Generate a boxplot of MFI (median fluorescence intensity) for TockyKmeansRF Feature Clusters

This function visualises marker MFI offeature clusters, other Timer+ cells, and Timer negative cells

Usage

plotClusterMFI(
  x,
  res_tockyrf,
  group = NULL,
  variables = NULL,
  min_cells = 10,
  Timer_positive = FALSE
)

Arguments

x

A `TockyPrepData` object containing the original flow cytometry data.

res_tockyrf

A list object output from `TockyKmeansRF`, which has been further processed using `ClusteringFeatureCells`.

group

Optional. A charaacter vector with the length one when the corresponding group only should be plotted. The default is NULL, which option uses all samples and groups.

variables

Optional. A charaacter vector to specify which variables are to be visualised.

min_cells

Numeric. The minimum nunmber of cells within a cluster to be analysed. The default is 10.

Timer_positive

Logical. Whether to remove Timer negative cells.

Examples

if (FALSE) { # \dontrun{
  data <- data.frame(Angle = runif(100), Intensity = runif(100))
  cell_cluster_id <- dbscan(data, eps = 0.1, minPts = 5)$cluster
  plotClusterMFI(data, cell_cluster_id)
} # }