| This tool is similar to our heat_map_creation tool but has many advanced options not provided in the basic tool. Similar to the basic tool, heat_map_creation_advanced is used to generate a clustered Heat Map from a data matrix, with many options for clustering. The input matrix is required to have labels in the first column and the first row containing. For example, column headers could be patient IDs and row headers (first column) could contain gene symbols. Covariate files add additional information bars to the heat map. For example, a patients smoking status could be provided as a covariate file. Any input covariate bar files must have the same row or column labels as in the input matrix to associate the covariate information with the appropriate row or column. The output is a compressed ngchm file that can be displayed in the NG-CHM viewer. To access the viewer in Galaxy, use the visualize icon at the bottom of the Galaxy History NG-CHM tool output file. Expand the History output file, then at the bottom are several icons the order being -- the save icon, information "I", rerun, then the Visualization (a chart looking icon). Hover over it, and select the 'NG-CHM Heat Map Viewer' option. The Heat Map will display in the Galaxy middle pane.
Additionally, the advanced tool allows for definition of row/column data types (e.g. Hugo Gene Symbol) and map attributes that enable the viewer to provide link outs from row/column labels to external resources with specific information about the selected row/columns (e.g. Gene Cards). The advanced tool is also capable of generating a covariate bar that identifies primary groupings based on the clustering dendrograms.
Please see Installing NG-CHM from the Galaxy Toolshed and Creating Heat Maps in Galaxy videos in our YouTube channel https://www.youtube.com/channel/UCADGir2q8IaI9cGQuzjSL9w
Full Documentation: http://bioinformatics.mdanderson.org/main/NG-CHM-V2:Overview
To access a suite of Galaxy Matrix Manipulation algorithms prior to Heat Map generation, search the Galaxy Tool Shed for “matrix_manipulation” The Galaxy visualization component does not install automatically. If you have not already installed the NG-CHM viewer with the heat_map_creation tool, you will need to run the following commands in terminal mode: NOTE: The following assumes /galaxy-central is the home directory for your Galaxy instance, otherwise replace /galaxy-central with your Galaxy instance's root directory. 1) mv /galaxy-central/../shed_tools/toolshed.g2.bx.psu.edu/repos/md-anderson-bioinformatics/heat_map_creation/*/heat_map_creation/mda_heatmap_viz.zip /galaxy-central/config/plugins/visualizations/ 2) cd /galaxy-central/config/plugins/visualizations/ 3) unzip mda_heatmap_viz.zip Then you must restart Galaxy for the visualization portion to take effect. 4) cd /galaxy-central 5) sh run.sh Remember Users MUST be logged into Galaxy to be able to see the heat map visualization component icon. The NG-CHM Heatmap Generator will run even if you are not logged into Galaxy. 6) Select NG-CHM tool from the toolshed and click install. It says R and Java dependencies are missing. Click install anyway. During install it says it is installing dependencies. 7) Follow the instructions to copy / unzip ng-chm code to the correct directory (note: the basic Galaxy Docker container does not have unzip but putting R on the machine includes it also.) Possible issues regarding dependencies that should not normally occur but have been documented. 8) R v3.4 and Java v1.8 are still missing so install them manually. For example using Ubuntu. If using Docker, first go into the container ‘docker exec –it <galaxy container name> /bin/bash’ From the command line: apt-get update apt-get install -y r-base apt-get install -y software-properties-common python-software-properties add-apt-repository -y ppa:openjdk-r/ppa apt-get update apt-get install -y openjdk-8-jdk update-alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java NOTE: these commands are specific to the Ubuntu OS release that the Docker GalaxyProject supplied container is built on. For other users running Galaxy in different environments the commands will vary. Search the internet for specifics. |
hg clone https://toolshed.g2.bx.psu.edu/repos/md-anderson-bioinformatics/heat_map_creation_advanced
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Create Clustered Heat Maps with Advanced Options | 2.14.0 | 16.01 | |