Next.Gen.Cluster.Heat.Map.Builder

A GenePattern Module to build Next-Generation Clustered Heat Maps (NG-CHMs) in GenePattern Notebook. For details about NG-CHM, please check NG-CHMs website

Description

Clustered heat maps are the most frequently used graphics for visualization of molecular profiling data in biology, appearing in many thousands of publications—but as static images.

To provide more capability for exploration of large data matrices, we developed highly interactive “Next-Generation” Clustered Heat Maps (NG-CHMs). NG-CHMs enable the user to zoom and navigate dynamically and link out to dozens of external data resources and tools. NG-CHMs exploit recent advances in web technology to improve performance, provide a highly-responsive user experience, and facilitate deep exploration of the biology (or other science) behind the image.

NG-CHMs include the following interactive capabilities (among many others):

• Extreme zooming without loss of resolution for drill-down into big data matrices.
• Fluent navigation.
• Link-outs from labels or pixels to a variety of pertinent annotation resources, including GeneCards, PubMed, the Gene Ontology, Google, and cBioPortal.
• Flexible real-time recoloring.
• High-resolution graphics that meet the requirements of all major journals.
• Annotation with pathway data.
• Capture of all metadata necessary to reproduce any chosen state of the map, even months or years later.

Other NGCHM Builders (Galaxy Builder,R buidler or online builder).

Use Next.Gen.Cluster.Heat.Map.Builder with GenePattern Notebook

Basic usage:

1. After loading Next.Gen.Cluster.Heat.Map.Builder module into notebook, paste the URL of SampleMatrix into Input Filename field, or upload matrix of your choice from local.
2. Click on Run button to use default setting for the generation of heatmap.

3. Upon completion of building process, several files will be generated as shown below. The .ngchm file is the next generation clustered heatmap file.

4. View the .ngchm file with Next.Gen.Cluster.Heat.Map.Viewer module by copying the URL of .ngchm file and pasting into ngchm file input field in the viewer module.

Adding covariates

1. Paste the same SampleMatrix URL into Input Filename field.
2. Click on the plus sign at the bottom of the builder module cell to show the fields for adding covarites.
3. Paste the URL for Sample Row Covariate into Row Covariate Input and the URL for Sample Column Covariate into Column Covariate Input.
4. Choose the type of covariate, Row Categorial for row covariate, Column Continuous for column covariate.
5. Click on Run and view the heatmap with viewer as described above.

Input

Name	Description
input Filename	input file type .tsv,.gct,.cdt * .tsv: tab-deliminated matrix file * .gct: tab-deliminated matrix file with additional information * .cdt: reordered matrix file
Heat Map Name	Name of Heat map. If omitted, input Filename will be used.
Heat Map Description	Brief description of the data
Summary Method	Average, Mode, Sample
Row Ordering Options	Hierarchical(default), Original, Random
Row Distance Metric	manhattan, euclidean(default), maximum, minkowski, correlation (Optional, required if row order method is Hierarchical)
Row Agglomeration Method	average, complete, single, ward.D(default), mcquitty (Optional, required if row order method is Hierarchical)
Row Label Type	Label the row names to view linkouts in the viewer, for example choose Gene Hugo Symbol.
gtr file	Gene tree file, records the order in which rows were joined. If gtr file is provided, then cdt file is required. (Optional, if you have gtr and cdt file generated from Hierarchical cluster module or other tools, you could upload files and convert them into ngchm.)
Column Ordering Options	Hierarchical(default), Original, Random
Column Distance Metric	manhattan, euclidean(default), maximum, minkowski, correlation (Optional, required if column order method is Hierarchical)
Column Agglomeration Method	average, complete, single, ward.D(default), mcquitty (Optional, required if column order method is Hierarchical)
Column Label Type	Label the column names to view linkouts in the viewer, for example choose Gene Hugo Symbol.
atr file	Array tree file, records the order in which columns were joined. If atr file is provided, then cdt file is required. (Optional, if you have atr and cdt file generated from Hierarchical cluster module or other tools, you could upload files and convert them into ngchm.)
Row Covariate Name	Name of the row covariate.(Optional)
Row Covariate Input	tsv file with row label and covariate value on each line.(Optional)
Row Covariate Type	discrete, continuous (Optional)
Column Covariate Name	Name of the column covariate.(Optional)
Column Covariate Input	tsv file with column label and covariate value on each line.(Optional)
Column Covariate Type	discrete, continuous (Optional)
Output Base Name	Name of output ngchm file, if omitted, input Filename will be used.

Output

Name	Description
ngchm file	.ngchm file, you could view the NGCHM with Next.Gen.Cluster.Heat.Map.Viewer module.
stderr.txt	error log
stdout.txt	processing log