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Snapshot-GUI User Manual

Prerequisites

  • pyqt5

Snapshot-GUI is based on PyQt5 and python 2.7.

We recommand three quick ways to install PyQt5 for your python 2.7.

1. Homebrew

You can install PyQt5 using Homebrew: brew install pyqt5.

2. Anaconda

  • Install Anaconda, and PyQt5 is included in Anaconda.

  • Download Anaconda: wget https://repo.continuum.io/archive/Anaconda2-5.1.0-MacOSX-x86_64.sh

  • Install Anaconda: bash Anaconda2-5.1.0-MacOSX-x86_64.sh. Press Enter and answer yes if questions are asked to install Anaconda in default directory.

  • Enable Anaconda PATH: bash ~/.bash_profile

PyQt5 is included in Anaconda.

3. Install from source (need sudo)

Install PyQt5 from PyQt5 official website

Get Start

To start Snapshot-GUI, run command python ./bin/gui/main.py. Figure 1 illustrate the Snapshot-GUI start window.

Figure 1

Use Snapshot-GUI

1. choose input directory.

Click the Choose Directory button for Input Directory to choose input directory.

The input directory should contains necessary input files and directories, as illustrated in Figure 2:

  • function_label fold
  • atac_sig fold
  • atac_pick fold
  • signal_list.txt file
  • peak_list.txt file
  • function_list.txt file
  • function_color_list.txt file
  • cd_tree.txt file

Figure 2

2. choose output directory.

Click the Choose Directory button for Output Directory to choose output directory. All analysis results will be saved in output directory.

3. preprocessing

Click the Preprocess button to check the input and output directories. Please make sure the input and output directories are chosen before preprocessing, otherwise, you will get warning as in Figure 3.

Figure 3

After preprocessing, the OK button is able to use, and the Change Display Color and Change Parameters buttons are also able to use, as illustrated in Figure 4.

Figure 4

4. change parameters and display colors

You can change parameters and display colors by click Change Parameters and Change Display Color button.

5. analyze your data

Click OK button to analyze your data, the Snapshot-GUI will automatically analyze your data in background, the progress bar is used to indicate the analysis progress, as shown in Figure 5.

Figure 5

6. visualize the result

When the data analysis finishes, the visualization window will pop out automatically, as illustrated in Figure 6.

Figure 6

The default visualization is Index-set mean signal heatmap (as in Figure 6). You can also choose to visualize the Index-set most frequent functional annotation heatmap, as shown in Figure 7.

Figure 7

7. collect results

All analysis results are stored in output directory, as illustrated in Figure 8.

Figure 8