Clinical Heatmap — clinicalheatmap • ClinicoPath

Clinical Heatmap

Usage

clinicalheatmap(
  data,
  rowVar,
  colVar,
  valueVar,
  annotationCols,
  annotationRows,
  scaleMethod = "none",
  clusterRows = TRUE,
  clusterCols = TRUE,
  colorPalette = "viridis",
  showRownames = TRUE,
  showColnames = TRUE,
  naHandling = "exclude",
  showDataSummary = TRUE,
  showInterpretation = TRUE,
  exportWidth = 8,
  exportHeight = 6,
  clusterDistanceRows = "euclidean",
  clusterMethodRows = "complete",
  clusterDistanceCols = "euclidean",
  clusterMethodCols = "complete",
  annotationType = "tile",
  addLayer = FALSE,
  layerType = "point",
  layerFilter = "",
  splitRows = 1,
  splitCols = 1,
  findOptimalK = FALSE,
  kRange = "2:8",
  exportRowClusters = FALSE,
  exportColClusters = FALSE,
  rowClusterPrefix = "RowCluster",
  colClusterPrefix = "ColCluster",
  survivalAnalysis = FALSE,
  survivalTime,
  survivalEvent,
  survivalEventLevel,
  clusterComparison = FALSE,
  comparisonVars
)

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.
exportWidth: Width of exported heatmap in inches.
exportHeight: Height of exported heatmap in inches.
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.
addLayer: Add a symbol layer on top of the heatmap.
layerType: Type of symbol to add as a layer.
layerFilter: Logical expression to filter which cells show symbols (e.g., "> 0.5").
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$assumptions`					a html
`results$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