PlotHeatMap2: Plot heatmap visualization for time-series data

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Plot heatmap visualization for time-series data

Description

Plot heatmap visualization for time-series data

Usage

PlotHeatMap2(
  mSetObj = NA,
  imgName,
  dataOpt = "norm",
  scaleOpt = "row",
  format = "png",
  dpi = 72,
  width = NA,
  smplDist = "pearson",
  clstDist = "average",
  colorGradient = "npj",
  fzCol,
  fzRow,
  fzAnno,
  annoPer,
  unitCol,
  unitRow,
  rankingMethod = "mean",
  topFeature = 2000,
  useTopFeature = F,
  drawBorder = T,
  show.legend = T,
  show.annot.legend = T,
  showColnm = T,
  showRownm = F,
  maxFeature = 2000
)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
imgName	Input a name for the plot
dataOpt	dataOpt, default is "norm"
scaleOpt	scaleOpt
format	Select the image format, "png", or "pdf".
dpi	Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images, the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
width	Input the width, there are 2 default widths, the first, width = NULL, is 10.5. The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.
smplDist	Select distance measure: euclidean, pearson, or minkowski
clstDist	Select clustering algorithm: ward, average, complete, single
colorGradient	Select heatmap colors: bwm, gray
rankingMethod	rankingMethod
topFeature	topFeature
useTopFeature	Use significant features only: F or T (default false)
drawBorder	Show cell borders: F or T (default F)
viewOpt	Select overview or detailed view: overview or detail
includeRowNames	includeRowNames, logical

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on April 20, 2024, 8:13 p.m.