met.plot_CorrHeatMap_Features: Pattern hunter, plot correlation heatmap

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Pattern hunter, plot correlation heatmap

Description

met.plot_CorrHeatMap_Features visualizes the correlations between features.

Usage

met.plot_CorrHeatMap_Features(
  mSetObj = NA,
  imgName = "correlation_features",
  format = "pdf",
  dpi = NULL,
  width = NA,
  cor.method = "pearson",
  colors = "bwm",
  viewOpt = "overview",
  fix.col = TRUE,
  no.clst = FALSE,
  corrCutoff = 0,
  plot = TRUE,
  export = TRUE
)

Arguments

mSetObj	Input name of the created mSet object.
imgName	(Character) Enter a name for the image file (if export = TRUE).
format	(Character, "png" or "pdf") image file format (if export = TRUE).
dpi	(Numeric) resolution of the image file (if export = TRUE). If NULL, the resolution will be chosen automatically based on the chosen file format (300 dpi for PNG, 72 dpi for PDF)
width	(Numeric) width of the the image file in inches (if export = TRUE).
cor.method	Indicate the correlation method, 'pearson', 'spearman', or 'kendall'.
colors	Indicate the colors for the heatmap, "bwm" for default, "gbr" for red/green, "heat" for heat colors, "topo" for topo colors, and "gray" for gray scale.
viewOpt	Indicate "overview" to get an overview of the heatmap, and "detail" to get a detailed view of the heatmap.
fix.col	(Logical) Fix colors (TRUE) or not (FALSE).
no.clst	(Logical) Indicate if the correlations should be clustered (TRUE) or not (FALSE).
corrCutoff	set correlation cut off
plot	(Logical, TRUE or FALSE) Shall the plot be returned in the RStudio 'Plots' pane?
export	(Logical, TRUE or FALSE) Shall the plot be exported as PDF or PNG file?

Value

The input mSet object with added heat map showing the correlations between features. The plot can be retrieved from within R via print(mSetObj$imgSet$corr.heatmap_features.plot).

Author(s)

Nicolas T. Wirth [e-mail] Technical University of Denmark License: GNU GPL (>= 2)

References

adapted from PlotCorrHeatMap (https://github.com/xia-lab/MetaboAnalystR).

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.