types

Documentation

Overview

Package types contains type declarations.

Index

• Constants
• type Analysis
• type Annotation
• type AnnotationPosition
• type Annotations
• type Marker
• type Markers
• type Matrices
• type ScatterAxesLabels
• type ScatterPlot
• type ScatterPoint
• type Settings

Constants

const HclustIgnore = 250000

HclustIgnore setting to skip clustering for nodes with this many comparisons to make.

Types

type Analysis

type Analysis struct {
	Columns  map[string]string
	Data     []map[string]string
	Settings Settings
}

Analysis files, file settings, analysis settings and column mapping.

type Annotation

type Annotation struct {
	Position AnnotationPosition
	Text     string
}

Annotation is the struct for heatmap annotation text.

type AnnotationPosition

type AnnotationPosition struct {
	X float64
	Y float64
}

AnnotationPosition is the x,y position for an annotation.

type Annotations

type Annotations struct {
	FontSize int
	List     map[string]Annotation `json:"list"`
}

Annotations is the struct for heatmap annotations.

type Marker

type Marker struct {
	Height int
	Width  int
	X      float64
	Y      float64
}

Marker is the struct for heatmap marker boxes.

type Markers

type Markers struct {
	Color string
	List  map[string]Marker `json:"list"`
}

Markers is the struct for heatmap markers.

type Matrices

type Matrices struct {
	Abundance, Ratio, Score [][]float64
	Conditions, Readouts    []string
}

Matrices holds input data formatted as matrices.

type ScatterAxesLabels

type ScatterAxesLabels struct {
	X string `json:"x"`
	Y string `json:"y"`
}

ScatterAxesLabels are labels for the x and y axis.

type ScatterPlot

type ScatterPlot struct {
	Labels ScatterAxesLabels `json:"labels"`
	Name   string            `json:"name"`
	Points []ScatterPoint    `json:"points"`
}

ScatterPlot contains data for a scatter plot

type ScatterPoint

type ScatterPoint struct {
	Color string  `json:"color"`
	Label string  `json:"label"`
	X     float64 `json:"x"`
	Y     float64 `json:"y"`
}

ScatterPoint contains data for a point on a scatter plot

type Settings

type Settings struct {
	// Shared settings
	Abundance                    string
	Condition                    string
	Control                      string
	Files                        []string
	LogBase                      string
	MinAbundance                 float64
	MinConditions                int
	MockConditionAbundance       bool
	Normalization                string
	NormalizationReadout         string
	ParsimoniousReadoutFiltering bool
	Png                          bool
	PrimaryFilter                float64
	Readout                      string
	ReadoutLength                string
	Score                        string
	ScoreType                    string
	SecondaryFilter              float64
	Type                         string

	// circheatmap
	ConditionMap   string
	Known          bool
	KnownFile      string
	OtherAbundance []string
	Species        string
	TissueFile     string
	Tissues        []string

	// condition-condition
	ConditionX string
	ConditionY string

	// correlation
	ConditionAbundanceFilter  float64
	ConditionScoreFilter      float64
	Correlation               string
	CytoscapeCutoff           float64
	IgnoreSourceTargetMatches bool
	ReadoutAbundanceFilter    float64
	ReadoutScoreFilter        float64
	UseReplicates             bool

	// dotplot
	AbundanceCap        float64
	BiclusteringApprox  bool
	Clustering          string
	ClusteringMethod    string
	ClusteringOptimize  bool
	ConditionClustering string
	ConditionList       []string
	Distance            string
	EdgeColor           string
	FillColor           string
	InvertColor         bool
	ReadoutClustering   string
	ReadoutList         []string
	XLabel              string
	YLabel              string
	WriteDistance       bool
	WriteHeatmap        bool

	// specificity
	SpecificityMetric string
}

Settings contains tool-specific analysis settings.