BuildHeatmap | R Documentation |
BuildHeatmap summarizes MetaDeconfound output in a heatmap or cuneiform plot
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"
)
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" |
for more details and explanations please see the package vignette.
ggplot2 object
data(reduced_feature)
data(metaMatMetformin)
example_output <- MetaDeconfound(featureMat = reduced_feature,
metaMat = metaMatMetformin,
logLevel = "ERROR")
plotObject <- BuildHeatmap(example_output)
alternativePlot <- BuildHeatmap(example_output, coloring = 2, showConfounded = FALSE)
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