BuildHeatmap: BuildHeatmap

In TillBirkner/metadeconfoundR: Check Multiple Covariates for Potenial Confounding Effects

BuildHeatmap

Description

BuildHeatmap summarizes MetaDeconfound output in a heatmap or cuneiform plot

Usage

BuildHeatmap(
  metaDeconfOutput,
  q_cutoff = 0.1,
  d_cutoff = 0.01,
  cuneiform = FALSE,
  coloring = 0,
  showConfounded = TRUE,
  intermedData = FALSE,
  featureNames = NULL,
  metaVariableNames = NULL,
  d_range = "fit",
  d_col = c("blue", "white", "red"),
  keepMeta = NULL,
  keepFeature = NULL,
  trusted = c("OK_sd", "OK_nc", "OK_d", "AD"),
  tileBordCol = "black",
  reOrder = "both"
)

Arguments

metaDeconfOutput	output of a metadeconfound run
q_cutoff	optional FDR-value cutoff used to remove low-significance entries from data
d_cutoff	optional effect size cutoff used to remove low effect size entries from data
cuneiform	optional logical parameter, plot cuneiform instead of heatmap when cuneiform = TRUE
coloring	optional, can be 0,1,2; 0: color all tiles according to effectsize ; 1: don't color not significant tiles 2: like 1 but also don't color confounded signal tiles
showConfounded	optional logical parameter; set to FALSE to remove significance markers from confounded signals
intermedData	only return intermediate data for plotting, default = FALSE
featureNames	optional two-column-dataframe containing corresponding "human-readable" names to the "machine-readable" feature names used as row.names in metaDeconfOutput. These human readable names will be displayed in the final plot. First column: machine-readable, second column: human-readable.
metaVariableNames	optional two-column-dataframe containing corresponding "human-readable" names to the "machine-readable" metadata names used as column names in metaDeconfOutput. These human readable names will be displayed in the final plot. First column: machine-readable, second column: human-readable.
d_range	range of effect sizes shown; "full": (default) range from -1 to +1; "fit": range reduced according to maximum and minimum effect size present in resulting plot
d_col	set color range for effect size as c(minimum, middle, maximum), default c("red", "white", "blue")
keepMeta	character vector of metavariable names (corresponding to names in metaDeconfOutput), that should be shown in resulting plot, even when they have no associations passing d_cutoff and q_cutoff
keepFeature	character vector of metavariable names (corresponding to names in metaDeconfOutput), that should be shown in resulting plot, even when they have no associations passing d_cutoff and q_cutoff
trusted	character vector of confounding status labels to be treated as trustworthy, not-confounded signal. default = c("OK_sd", "OK_nc", "OK_d", "AD")
tileBordCol	tile border color of heatmap tiles, default: "black"
reOrder	reorder features and/or metadata? possible options: c("both", "feat", "meta", "none"), default: "both"

Details

for more details and explanations please see the package vignette.

Value

ggplot2 object

Examples

data(reduced_feature)
data(metaMatMetformin)

example_output <- MetaDeconfound(featureMat = reduced_feature,
                                  metaMat = metaMatMetformin)

plotObject <- BuildHeatmap(example_output)
print(plotObject)

alternativePlot <- BuildHeatmap(example_output, coloring = 2, showConfounded = FALSE)
print(alternativePlot)

TillBirkner/metadeconfoundR documentation built on Sept. 3, 2023, 9:11 a.m.