romicsHeatmap: romicsHeatmap()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsHeatmap()

Description

Plots a scaled heatmap of the data layer from a romics_object using the function heatmaps.2 from the package gplots. This data can (or not) be filtered based on the statistics layer of the romics_object.

Usage

romicsHeatmap(
  romics_object,
  color_palette = viridis(20),
  color_boundaries = c(-2, 2),
  sample_hclust = TRUE,
  sample_hclust_method_dist = "euclidean",
  sample_hclust_method_hclust = "ward.D",
  variable_hclust = TRUE,
  variable_hclust_method_dist = "euclidean",
  variable_hclust_method_hclust = "ward.D",
  variable_hclust_number = 1,
  ANOVA_filter = "none",
  p = 0.05,
  statCol = "none",
  statCol_filter = "<=0.05",
  statCol2 = "none",
  statCol2_filter = "<=0.05",
  notecol = "black",
  density.info = "none",
  trace = "none",
  labRow = FALSE,
  cexCol = 1,
  margins = c(15, 5),
  key.title = "Scaled Heatmap",
  key.xlab = "Z-scores",
  RowSideColor = "ANOVA_p",
  ...
)

Arguments

romics_object	A romics_object created using romicsCreateObject().
color_palette	Character vector of colors. By default the viridis(n=20) will be used
color_boundaries	Numerical vector of length 2. Indicates the min and max of the color scale. By default will be c(-2,2)
sample_hclust	Boolean. Indicates if hclust has to be done for the samples.
sample_hclust_method_dist	Sample dist method to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman" or "kendall".
sample_hclust_method_hclust	Sample agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid".
variable_hclust	Boolean. Indicates if hclust has to be done for the variables.
variable_hclust_method_dist	Variable dist method to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman" or "kendall".
variable_hclust_method_hclust	Variable agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid".
variable_hclust_number	Numerical of length 1. Indicates the number of clusters to be used for the coloring of the variable hclust
ANOVA_filter	Either 'none', 'p' or 'padj'. Indicates if an the ANOVA filter has to be used to plot the Heatmap (only the features below the filter will be displayed on the heatmap)
p	Numerical of length 1 indicating the value of the ANOVA_filter cutoff (anything below this value will be conserved).
statCol	A column contained in the statistical layer of the romics_object, the list of columns can be obtained by using the function romicsCalculatedStats().
statCol_filter	Character to indicate how this column should be filtered (e.g. '<=0.05','>0.05','==1', '==TRUE', '>2')
statCol2	A column contained in the statistical layer of the romics_object, the list of columns can be obtained by using the function romicsCalculatedStats().
statCol2_filter	Character to indicate how this column should be filtered (e.g. '<=0.05','>0.05','==1', '==TRUE', '>2')
notecol	(optional) character string specifying the color for cellnote text. Defaults to "black".
density.info	character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key.
trace	has to be in c("column","row","both","none"). See trace() documentation.
cexCol	positive numbers, used as cex.axis in for the row or column axis labeling. The defaults currently only use number of columns.
key.title	main title of the color key. If set to NA no title will be plotted.
key.xlab	x axis label of the color key. If set to NA no label will be plotted.
RowSideColor	character vector has to be either 'none' or a calculated statistics (ending by _p or _padj) from the romics_object
...	parameters to send to heatmap.2
LabRow	character vectors with row labels to use; these default to rownames(x)
margin	numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively.

Details

Create a customizable and filterable heatmap based on the romics_object statistics Layer. the ANOVA filter enables to restrict the variable displayed to be only the ones passing an ANOVA

2 stat column filters (StatCol) can be set simultaneously to restrict the variable displayed. Each filter enable to sort based on a given column of the statistics layer (statCol_filter) of an romics_object (the list of columns can be obtained by using the function romicsCalculatedStats()) using a specific text (statCol_text) this text indicate what parameter should be used to filter this column (example: column has to be positive -> statCol_text= '>0'). Note that the ANOVA filter is applied first (if any) and then the filters are applied sequencially (first, then second, then third).

Value

A heatmap generated using the gplots::heatmap.2() function. Subsequently any adjustment of the heatmap.2 can be performed as described in gplots::heatmap.2() documentation.

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.