Heatmap

Description

Performs hierarchical clustering on both the samples (rows) and variables (columns) of the dataMatrix

Displays the dataMatrix with sorted rows and samples and the dendrograms (heatmap)

In the output dataMatrix, sampleMetadata and variableMetadata files sample and variables are sorted according to the dendrograms

Optionally, indicates the groups of samples and/or variables obtained by cutting the dendrograms into a specific number of partitions

Note: 1) Computations rely on the 'hclust' function. The dissimilarity is 1 - cor (where cor is the Spearman correlation) and the 'ward.D' aggregating method is used.

2) A "blue-orange-red" palette is generated with the function 'colorRampPalette'; By default, variables are standardized (mean-centered and unit-scaled) to enhance contrast on the figure; standardization can be turned off by using the full list of parameters; in any case, standardizing is performed after the computation of clusters, for display only

3) When a specific number of sample and/or variable groups (i.e. > 1) are selected, the group numbers are indicated on the plot and in an additional 'heat_clust" column in the sampleMetadata and/or variableMetadata

4) Example of computation times: for 126 variables: a few seconds; for 4324 variables: 30 min

Workflow position

Input files

Parameters

Number of sample clusters

By default (cluster = 1), only dendrograms are displayed; when a specific number of sample clusters is selected, the sample dendrogram is cut at the corresponding level: the sample groups are displayed on the dendrogram and a "heat_clust" column is added in the sampleMetadata file with the group of each sample

Number of variable clusters

Same as above for variables

Standardization (Full list)

By default, variables are standardized for display to enhance contrast of the heatmap (note that standardization is performed after the clustering for display only and does not modify cluster computation nor intensities in the output files)

Size of labels (Full list)

The size of sample and variable names on the heatmap is 0.8 (note that names with more than 14 characters are truncated); this number may be lowered (or uppered) in case of many (few) names to display

Output files

dataMatrix_out.tabular

dataMatrix file with rows and columns sorted according to the dendrogram

sampleMetadata_out.tabular

sampleMetadata file with rows sorted according to the sample dendrogram; in case a number of sample groups is specified, and additional "heat_clust" column is added with the cluster group of each sample

variableMetadata_out.tabular

variableMetadata file with rows sorted according to the variable dendrogram; in case a number of variable groups is specified, and additional "heat_clust" column is added with the cluster group of each variable

figure.pdf

Heatmap

information.txt

File with all messages and warnings generated during the computation

Working example

See the W4M00001a_sacurine-subset-statistics shared history in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)

NEWS