Component: HeatMapReport

HeatMapReport

Clusters samples hierarchically and draws the corresponding dendrograms and heat map. The clustering is determined by the input matrix and the clustering parameter.

The size and character expansion factor of row and column names, color scheme and number of colors of the heat map, and the image margin sizes can all be adjusted.

The component outputs a LaTeX report fragment.

Version	3.0
Bundle	tools
Categories
Authors	Riku Louhimo (Riku.Louhimo@Helsinki.FI), Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)
Issue tracker	View/Report issues
Requires	R ; pheatmap (R-package)
Source files	component.xml HeatMap.r
Usage	Example with default values HeatMapReport( in = Matrix, //rowLabels = CSV, //colLabels = CSV, caption = "", clusterMethod = "average", colorScheme = "colorRampPalette(c('blue','white','red'))((256))", custom = "", distanceMetric = "euclidean,euclidean", drawColnames = true, drawLegends = false, drawRownames = true, fontSizeCol = 10.0, fontSizeRow = 10.0, marginCol = 7, marginRow = 4, plotHeight = 5, plotWidth = 10, scale = "none", sectionTitle = "Sample clusters", sectionType = "subsection", visualScales = false, width = 16 )

Version

3.0

Bundle

tools

Categories

Authors

Riku Louhimo (Riku.Louhimo@Helsinki.FI), Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)

Issue tracker

View/Report issues

Requires

R ; pheatmap (R-package)

Source files

component.xml HeatMap.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
in	Matrix	Mandatory	Numeric data matrix.
rowLabels	CSV	Optional	Annotation for matr rows. Unique colors are assigned to each unique group in label matrix and plotted next to the dendrogram. Values in rowLabels do not have to be in the same order as rows in matr input. Annotation column names cannot be names 'Col1', 'Col2',..., 'ColN' due to a bug in the pheatmap library.
colLabels	CSV	Optional	Annotation for matr columns. Unique colors are assigned to each unique group in label matrix and plotted beneath the dendrogram. Values in colLabels do not have to be in the same order as columns in matr input. Annotation column names cannot be names 'Col1', 'Col2',..., 'ColN' due to a bug in the pheatmap library.

Name

Type

Mandatory

Description

Matrix

Mandatory

Numeric data matrix.

rowLabels

CSV

Optional

Annotation for matr rows. Unique colors are assigned to each unique group in label matrix and plotted next to the dendrogram. Values in rowLabels do not have to be in the same order as rows in matr input. Annotation column names cannot be names 'Col1', 'Col2',..., 'ColN' due to a bug in the pheatmap library.

colLabels

CSV

Optional

Annotation for matr columns. Unique colors are assigned to each unique group in label matrix and plotted beneath the dendrogram. Values in colLabels do not have to be in the same order as columns in matr input. Annotation column names cannot be names 'Col1', 'Col2',..., 'ColN' due to a bug in the pheatmap library.

Name	Type	Description
out	Latex	Clustering report.

Name

Type

Description

out

Latex

Clustering report.

Parameters

Name	Type	Default	Description
caption	string	""	Image caption.
clusterMethod	string	"average"	Hierarchical clustering method to be used. One of 'average', 'complete', 'ward', 'single', 'mcquitty', 'median' or 'centroid'. See the hclust R function help for a complete description of the alternatives. The same method applies to both columns and rows.
colorScheme	string	"colorRampPalette(c('blue','white','red'))((256))"	Color palette used for the heatmap hues. One of 'cm', 'heat', 'topo', 'terrain', 'redblue' and 'redgreen'; or an R expression producing a vector of colors. For the R expression, the number of colors is set as specified by each function.
custom	string	""	A comma separated list of 'parameter=value' pairs that are passed to pheatmap AS THEY ARE. This allows customising the heatmap command. Parameters and values are not checked so use with caution.
distanceMetric	string	"euclidean,euclidean"	Distance measure to be used in computing distances from the input matrix for the clustering. One of 'pcc', 'euclidean', 'manhattan', 'maximum', 'canberra', 'binary', 'minkowski', or 'none' if no reordering should be done. The parameter is a comma separated list of lenght two. The first value defines the metric for rows and the second value for columns. Setting either value 'NA' disables clustering and dendrogram for rows or columns. The special value 'NA,NA' disables clustering for both rows and columns. The default metric is the Euclidian distance.
drawColnames	boolean	true	Enable or disable column names in the plot.
drawLegends	boolean	false	Enable or disable legends for row and column labels in the plot.
drawRownames	boolean	true	Enable or disable row names in the plot.
fontSizeCol	float	10.0	Font size for column names.
fontSizeRow	float	10.0	Font size for row names.
marginCol	int	7	The margin size on the x-axis (input matrix columns).
marginRow	int	4	The margin size on the y-axis (input matrix rows).
plotHeight	int	5	The height of graphic region in inches.
plotWidth	int	10	The width of graphic region in inches.
scale	string	"none"	Indicates how centering and scaling will be performed. The possible values are "none","row", or "column". By default, the distance matrix is calculated from the scaled values (see 'visualScales' parameter).
sectionTitle	string	"Sample clusters"	Title of the LaTeX section.
sectionType	string	"subsection"	Type of LaTeX section: usually one of section, subsection or subsubsection. If empty, no section statement is written.
visualScales	boolean	false	Indicates whether the distance matrix is calculated from scaled or unscaled values. This is useful especially when the data need to be clustered based on the raw values but scaling creates more a visually cleared figure.
width	float	16	Absolute width of the diagram in centimeters.

Name

Type

Default

Description

caption

string

Image caption.

clusterMethod

string

"average"

Hierarchical clustering method to be used. One of 'average', 'complete', 'ward', 'single', 'mcquitty', 'median' or 'centroid'. See the hclust R function help for a complete description of the alternatives. The same method applies to both columns and rows.

colorScheme

string

"colorRampPalette(c('blue','white','red'))((256))"

Color palette used for the heatmap hues. One of 'cm', 'heat', 'topo', 'terrain', 'redblue' and 'redgreen'; or an R expression producing a vector of colors. For the R expression, the number of colors is set as specified by each function.

custom

string

A comma separated list of 'parameter=value' pairs that are passed to pheatmap AS THEY ARE. This allows customising the heatmap command. Parameters and values are not checked so use with caution.

distanceMetric

string

"euclidean,euclidean"

Distance measure to be used in computing distances from the input matrix for the clustering. One of 'pcc', 'euclidean', 'manhattan', 'maximum', 'canberra', 'binary', 'minkowski', or 'none' if no reordering should be done. The parameter is a comma separated list of lenght two. The first value defines the metric for rows and the second value for columns. Setting either value 'NA' disables clustering and dendrogram for rows or columns. The special value 'NA,NA' disables clustering for both rows and columns. The default metric is the Euclidian distance.

drawColnames

boolean

true

Enable or disable column names in the plot.

drawLegends

boolean

false

Enable or disable legends for row and column labels in the plot.

drawRownames

boolean

true

Enable or disable row names in the plot.

fontSizeCol

float

10.0

Font size for column names.

fontSizeRow

float

10.0

Font size for row names.

marginCol

int

The margin size on the x-axis (input matrix columns).

marginRow

int

The margin size on the y-axis (input matrix rows).

plotHeight

int

The height of graphic region in inches.

plotWidth

int

The width of graphic region in inches.

scale

string

"none"

Indicates how centering and scaling will be performed. The possible values are "none","row", or "column". By default, the distance matrix is calculated from the scaled values (see 'visualScales' parameter).

sectionTitle

string

"Sample clusters"

Title of the LaTeX section.

sectionType

string

"subsection"

Type of LaTeX section: usually one of section, subsection or subsubsection. If empty, no section statement is written.

visualScales

boolean

false

Indicates whether the distance matrix is calculated from scaled or unscaled values. This is useful especially when the data need to be clustered based on the raw values but scaling creates more a visually cleared figure.

width

float

Absolute width of the diagram in centimeters.

Test cases

Test case	Parameters▼	IN in	IN rowLabels	IN colLabels	OUT out
case1	(missing)	in	(missing)	(missing)	out
case2	properties	in	(missing)	(missing)	out
	clusterMethod = complete, distanceMetric = NA,NA, colorScheme = rev(heat.colors(256)), marginRow = 5, marginCol = 10, fontSizeCol = 9, fontSizeRow = 9, width = 15, drawRownames = false, drawColnames = false
case3	properties	in	rowLabels	colLabels	(missing)
	distanceMetric = euclidean,euclidean, drawLegends = true, drawRownames = true, drawColnames = true, marginRow = 4
case4	properties	in	rowLabels	colLabels	(missing)
	distanceMetric = euclidean,euclidean, drawLegends = true, drawRownames = true, drawColnames = true, marginRow = 4, custom = cutree_rows=2,cutree_cols=2
case5	properties	in	rowLabels	colLabels	(missing)
	distanceMetric = euclidean,euclidean, drawLegends = true, drawRownames = true, drawColnames = true, marginRow = 4, visualScales=true

Test case

Parameters▼

IN
in

IN
rowLabels

IN
colLabels

OUT
out

case1

(missing)

(missing)

out

case2

properties

(missing)

out

clusterMethod = complete,
distanceMetric = NA,NA,
colorScheme = rev(heat.colors(256)),
marginRow = 5,
marginCol = 10,
fontSizeCol = 9,
fontSizeRow = 9,
width = 15,
drawRownames = false,
drawColnames = false

case3

properties

rowLabels

colLabels

(missing)

distanceMetric = euclidean,euclidean,
drawLegends = true,
drawRownames = true,
drawColnames = true,
marginRow = 4

case4

properties

rowLabels

colLabels

(missing)

distanceMetric = euclidean,euclidean,
drawLegends = true,
drawRownames = true,
drawColnames = true,
marginRow = 4,
custom = cutree_rows=2,cutree_cols=2

case5

properties

rowLabels

colLabels

(missing)

distanceMetric = euclidean,euclidean,
drawLegends = true,
drawRownames = true,
drawColnames = true,
marginRow = 4,
visualScales=true

Anduril

HeatMapReport

Inputs

Outputs

Parameters

Test cases