Clinical Heatmap

Clinical Heatmap

Usage

clinicalheatmap(
  data,
  rowVar,
  colVar,
  valueVar,
  annotationCols = NULL,
  annotationRows = NULL,
  scaleMethod = "none",
  clusterRows = FALSE,
  clusterCols = FALSE,
  colorPalette = "viridis",
  showRownames = FALSE,
  showColnames = FALSE,
  naHandling = "exclude",
  showDataSummary = FALSE,
  showInterpretation = FALSE,
  showSummary = TRUE,
  showWorkflow = FALSE,
  plotWidth = 800,
  plotHeight = 600,
  clusterDistanceRows = "euclidean",
  clusterMethodRows = "complete",
  clusterDistanceCols = "euclidean",
  clusterMethodCols = "complete",
  annotationType = "tile",
  splitRows = 1,
  splitCols = 1,
  findOptimalK = FALSE,
  kRange = "2:8",
  exportRowClusters = FALSE,
  exportColClusters = FALSE,
  rowClusterPrefix = "RowCluster",
  colClusterPrefix = "ColCluster",
  survivalAnalysis = FALSE,
  survivalTime = NULL,
  survivalEvent = NULL,
  survivalEventLevel,
  clusterComparison = FALSE,
  comparisonVars = NULL
)

Arguments

data

The dataset as a data frame containing the variables for analysis.

rowVar

A string naming the variable from data that will define the heatmap rows (e.g., patient IDs, gene names).

colVar

A string naming the variable from data that will define the heatmap columns (e.g., biomarkers, time points).

valueVar

A string naming the numeric variable from data that will be visualized in the heatmap.

annotationCols

Optional variables to use as column annotations (e.g., treatment groups, clinical stages).

annotationRows

Optional variables to use as row annotations (e.g., patient characteristics, gene families).

scaleMethod

Method for scaling the data values before visualization.

clusterRows

Whether to perform hierarchical clustering on rows.

clusterCols

Whether to perform hierarchical clustering on columns.

colorPalette

Color palette for the heatmap visualization.

showRownames

Whether to display row names in the heatmap.

showColnames

Whether to display column names in the heatmap.

naHandling

How to handle missing values in the data.

showDataSummary

Display a summary of the data structure and values.

showInterpretation

Display interpretation guidelines and clinical context.

showSummary

Display a plain-language summary suitable for clinical documentation and reports.

showWorkflow

Display step-by-step clinical workflow guidance for using heatmaps in practice.

plotWidth

Width of heatmap plot in pixels.

plotHeight

Height of heatmap plot in pixels.

clusterDistanceRows

Distance metric for row clustering.

clusterMethodRows

Agglomeration method for row clustering.

clusterDistanceCols

Distance metric for column clustering.

clusterMethodCols

Agglomeration method for column clustering.

annotationType

Type of annotation visualization for tidyHeatmap.

splitRows

Number of row groups to split based on dendrogram branches.

splitCols

Number of column groups to split based on dendrogram branches.

findOptimalK

Automatically determine optimal number of clusters using elbow method and silhouette analysis.

kRange

Range of K values to test (format: "min:max", e.g., "2:10").

exportRowClusters

Add row cluster assignments as a new column in the dataset.

exportColClusters

Add column cluster assignments as a new column in the dataset.

rowClusterPrefix

Name for the exported row cluster assignment column.

colClusterPrefix

Name for the exported column cluster assignment column.

survivalAnalysis

Perform survival analysis comparing row clusters (requires survival data).

survivalTime

.

survivalEvent

.

survivalEventLevel

.

clusterComparison

Compare clinical/molecular characteristics across discovered clusters.

comparisonVars

.

Value

A results object containing:

results$todo					a html
results$aboutAnalysis					a html
results$dataSummary$dataStructure					a table
results$dataSummary$valueSummary					a table
results$dataSummary$missingData					a table
results$heatmap					an image
results$annotations$columnAnnotations					a html
results$annotations$rowAnnotations					a html
results$interpretation					a html
results$clinicalSummary					a html
results$reportSentences					a html
results$plainSummary					a html
results$workflow					a html
results$assumptions					a html
results$optimalKAnalysis$elbowPlot					an image
results$optimalKAnalysis$silhouettePlot					an image
results$optimalKAnalysis$optimalKTable					a table
results$clusterAssignments$rowClusterTable					a table
results$clusterAssignments$colClusterTable					a table
results$clusterSurvival$kmPlot					an image
results$clusterSurvival$survivalTable					a table
results$clusterSurvival$logRankTest					a table
results$clusterCharacteristics$characteristicTable					a table
results$clusterCharacteristics$clusterInterpretation					a html