mdsplot: Create sample-level MDS plot

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

Description

Multi-Dimensional Scaling (MDS) plot computed across median marker expression in each sample or metadata grouping.

Usage

mdsplot(
  data,
  grouping = "group",
  feature = NULL,
  markers = NULL,
  colkey = NULL,
  legendPosition = "right",
  legendLabSize = 12,
  legendIconSize = 5,
  xlim = NULL,
  ylim = 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,
  title = "Metadata plot",
  subtitle = "",
  caption = "MDS Plot",
  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 = TRUE,
  gridlines.minor = TRUE,
  borderWidth = 0.8,
  borderColour = "black"
)

Arguments

data	a SingleCellExperiment.
grouping	a character string representaing which metadata slot to group the individual samples by.
feature	a character string represnting a feature to label the heatmap with.
markers	a character string specifying which markers to include.
colkey	a vector of grouping ids the colour strings to indicate the feature labelling.
legendPosition	a string for ggplot2 legend position.
legendLabSize	ggplot2 legend label size
legendIconSize	ggplot2 legend icon size
xlim	ggplot2 x limit specification
ylim	ggplot2 y limit specification
xlabAngle	specify the x lab angle
xlabhjust	Specify the horizontal justification of the x axis (0 = left jsutified, 1 = right justified)
xlabvjust	Specify the vertical justification of the x axis (0 = left jsutified, 1 = right justified)
ylab	specify the y axis label
ylabAngle	specify the y lab angle
ylabhjust	Specify the horizontal justification of the y axis (0 = left jsutified, 1 = right justified)
ylabvjust	Specify the vertical justification of the y axis (0 = left jsutified, 1 = right justified)
axisLabSize	specify the axis label size
title	specify the title text of the plot
subtitle	specify the subtitle text of the plot
caption	specify the caption text of the plot
titleLabSize	specify the title text size
subtitleLabSize	specify the subtitle text size
captionLabSize	specify the caption text size
stripLabSize	specify the facet labels of a plot

Value

a ggplot object.

Author(s)

James Opzoomer

Examples

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

# Generate sample level MDS plot with all markers
mdsplot(sce_gvhd, feature = "condition", colkey = c(None = 'royalblue', GvHD = 'red2'))

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