Data

File Format

The default data format for upload is a tab delimited text file with the following formatting:

  1. The first row should have the the name of columns (header)
  2. The first two columns are reserved for id (which should be unique) and name of the row.
  3. ALl the rows should have the same number of columns.
  4. All the columns should be sepearted by a tab

Snippet of data file for use with iCanPlot
idnamet-testfold
1427464_s_atHspa5-23.591.23
1419406_a_atBcl11a-21.963.12
1417138_s_atPolr2e-19.180.7
1437687_x_atFkbp9-18.914.51

Link to example file

Other supported file formats

  • GCT : text file format used for storing gene expression data

Excel files

Currently, upload of excel files is not supported. If you have data in an excel file, format it as described above, save it as a tab-delimited text file and then upload for plotting. Support for direct upload of excel file will be added in the future.

data.js

The text files are parsed using the script data.js. Developers may extend it to add support for other data types.

Parameters

Data Source

A single project may have multiple related data files. Using this option, a user may choose the specific data file to plot.

X axis, Y axis

They are required for the plot. You may choose any data columns for x and y axes.

Size, Color

These are optional. If enabled, the points are scaled and colored based on the values of the selected column.

Interacting with the Plot

Highlighting

The highlight box allows users to highlight points of choice. The highlighting is based on the name of the row in the data. If data source or x/y axis are changed after entering names in the highlight box, the same data points are highlighted again. This is useful to visualize the pattern of a geneset in different data set and for different variables.

Selection

Users may select a region of the plot to identify the points in them and analyze them on the fly. Selection can be done by defining a polygon of interest. Clicking defines the first point of the polygon. Moving your mouse and clicking defines the subsequent nodes of the polygon. Finally, double clicking closes the polygon and selects the points.

Analysis

If so configured, iCanPlot allows for on the fly analysis of the selected points. In this case, a geneset overlap analysis is done on the selected genes and the significantly enriched genesets are shown.