November 7th, 2012IGV search:
· Integrative Genomics Viewer (IGV) is a very powerful genomic browser that provides a complementary visualization of multidimensional genomics data to that of interactive heatmaps. Often it is useful to explore this type of data with the two tools at the same time. With that idea in mind we did a first step to integrate the two types of views. Using the IGV interface for other applications to send commands, Gitools can now locate any position within the human chromosome in your opened instance of IGV. In the screenshot we have the focus on the gene CPM (with the Ensembl id ENSG00000135678). If you click the link “Locate Id in genomic viewer (IGV)” in the left details panel, Gitools will locate the gene within IGV. If you have many genes selected, then Gitools will tell IGV to show them in split screen view.
Display name in color labels:
· As of version 1.7.0 it is possible to directly display the label name if you choose to add a header of the type Colored Labels from annotations to your heatmap. You can show the names by checking the “Show cluster names” box when adding a new header from annotations.
Adding data header from aggregated values:
· A new type of header can be added now to columns or rows: Aggregated heatmap from matrix data. In the screenshot we can see at (3) the mean expression values, calculated with the mean aggregation method for each row. The aggregation of the values can be calculated for the whole row, just for some selected columns or according to column annotations, as it is the case in the screenshot. Note that even though the mean expression values are shown in the rows annotations, the main heatmap is displaying alteration events.
Categorical scale and scale drawing:
· We have added a new color scale to Gitools: the categorical scale. It is designed to visualize categorical data, as shown in the screenshot. Each different data value is assigned to a color, which can be set by the user. The way that the color scales are drawn has been redesigned to be more intuitive.
August 29th, 2011
· The GO and KEGG importers work fine now for all the types of identifiers
· An exception when annotations don’t contain all the labels have been fixed
May 26th, 2011
· Windows users are not able to launch it from the zip by clicking on gitools.bat
· Filtering by labels doesn’t sort accordingly the filtered rows/columns