markerExpression: Generate an dotplot of a dimensionality reduction with marker...

In kordastilab/ImmunoCluster: Fast and accesible Immune profiling CyTOF data

Description

Generate an dotplot of a dimensionality reduction with marker expression overlaid as a heat dimension.

Usage

markerExpression(
  indata,
  layout = NULL,
  assay = "scaled",
  reducedDim = "UMAP",
  dimColnames = colnames(as.data.frame(reducedDim(indata, reducedDim))),
  markers = sample(rownames(indata), 6),
  ncol = 3,
  nrow = 2,
  col = c("darkblue", "yellow"),
  colMidpoint = 0,
  alpha = c(0, 1),
  pointSize = 0.5,
  legendPosition = "right",
  legendLabSize = 12,
  legendIconSize = 5,
  legendKeyHeight = 2.5,
  xlim = NULL,
  ylim = NULL,
  celllab = NULL,
  labSize = 3,
  labhjust = 1.5,
  labvjust = 0,
  drawConnectors = TRUE,
  widthConnectors = 0.5,
  colConnectors = "black",
  xlab = dimColnames[1],
  xlabAngle = 0,
  xlabhjust = 0.5,
  xlabvjust = 0.5,
  ylab = dimColnames[2],
  ylabAngle = 0,
  ylabhjust = 0.5,
  ylabvjust = 0.5,
  axisLabSize = 16,
  stripLabSize = 16,
  title = "Individual marker expression",
  subtitle = "",
  caption = ifelse(is(indata, "SingleCellExperiment"), paste0("Total cells, ",
    nrow(as.data.frame(reducedDim(indata, reducedDim))[!is.na(reducedDim(indata,
    reducedDim)[, 1]), ])), paste0("Total cells, ", nrow(layout))),
  titleLabSize = 16,
  subtitleLabSize = 12,
  captionLabSize = 12,
  hline = NULL,
  hlineType = "longdash",
  hlineCol = "black",
  hlineWidth = 0.4,
  vline = NULL,
  vlineType = "longdash",
  vlineCol = "black",
  vlineWidth = 0.4,
  gridlines.major = FALSE,
  gridlines.minor = FALSE,
  borderWidth = 0.8,
  borderColour = "black"
)

Arguments

indata	a SingleCellExperiment.
assay	the SCE assay to choose from.
reducedDim	a sting representing the dimensionality reduction stored in the SCE to plot
markers	a sting or vecotor of stings representing the markers to select for plotting
ncol	a numeric representing the number of colums to arrange the plots into
nrow	a numeric representing the number of rows to arrange the plots into
col	a vector of two strings representing the colour gradient to be used as the heat component on the expression plot
colMidpoint	a numeric representing the midpoint of the colour gradient specified in 'col', the default is 0
pointSize	a numeric specifying the point size of the dots on the plot, default is 0.5
plotting_options	The rest of the options can all found in the ggplot2 documentation. These options control various elements of the ggplot2 output.

Value

a SingleCellExperiment object.

Author(s)

Kevin Blighe, James Opzoomer [e-mail]

Examples

# Download complete ImmunoCluster SCE object from zenodo
sce_gvhd = readRDS(url("https://zenodo.org/record/3801882/files/sce_gvhd.rds"))

# Run UMAP and store in sce object
sce_gvhd = performUMAP(sce_gvhd)

expression_markers =  c('CD3', 'CD4', 'CD8a', 'CD11b', 'CD19', 'CD56')

exp_plot_umap = markerExpression(sce_gvhd,
                                markers = expression_markers,
                                reducedDim = 'UMAP',
                                title = 'UMAP',
                                nrow = 1, ncol = 6,
                                pointSize = 0.05,
                                legendKeyHeight = 1.0,
                                legendLabSize = 14,
                                stripLabSize = 20,
                                axisLabSize = 18,
                                titleLabSize = 20,
                                captionLabSize = 22)

kordastilab/ImmunoCluster documentation built on May 10, 2021, 7:41 a.m.