Thank you for choosing PanGraphViewer. Hope you can find our tool is useful for your study. In this section, we will introduce a general workflow
(see the figure below) that can be used to explore PanGraphViewer
.
There are three key functions that we would like to emphasize.
Depending on the purpose and preference, users can install either application on their platform.
Before starting the application, firstly, users need to prepare an rGFA
file, a GFA_v1
file or a VCF
file that can be directly imported into the application. An output directory is also needed when processing the analyses.
After specifying a needed file and an output directory, users can start to parse the file and then the graph information underlying would be stored in the memory. Users can adjust their purpose to decide which chromosome/sequence or a segment of it can be displayed in the display canvas by specifying the backbone
, chromosome/sequence
name, coordinates
or "nodeIDs"..
Once the graph is displayed, users can use, for example, the mouse
to zoom in and out to explore the graph. Hover information will show in the canvas if users move the mouse
to the node.
If users find some nodes are of interest, they can check or save the sequence of the nodes.
Usually, users can check nodes that are in variant hotspot regions or nodes falling in the gene model regions which may interrupt the genes and change the functions in some samples.
The saved node sequences can also be imported to other tools such as NCBI BLAST
to check the functions.
If users have the annotation file for the backbone
sample, they can check gene models that are interrupted by some sequences/nodes in some samples.
For the desktop-based
application, once it is opened as shown below, users can follow the following steps to explore the program.
Here we provide two options to let users select if they want to explore a GFA
-based graph or a VCF
-based graph.
When selecting to plot a GFA
-based graph, an rGFA
file or a GFA_v1
file is needed. Users can click the Select
button to specify the file and then select an output directory to perform the analyses.
When selecting to plot a VCF
-based graph, a VCF
file is needed.
Users can click the Select
button to specify the VCF file. An output directory is also needed to perform the analyses. Here the Backbone name
and Backbone fasta
are optional if
backbone fasta
The program will check automatically if the given VCF
file is a standard one once a fasta
file is not specified. If the VCF
file selected is not qualified, an error message will pop up.
Otherwise, a warning message will show.
By default the Backbone name
is backbone and the Threads
to parse the VCF file is 4
.
Once the files are selected and the output directory is specified, users can click the Start
button to parse either the given GFA
file or the VCF
file. The program will run internally with 'Parsing... or Converting ...' showing in the Status
bar. Once this is completed, 'Finished in xxx s!' will show.
After completing GFA
or VCF
parsing, users can go to the Selection for Plot
panel to check genome graphs. Here we provide Basic settings
and Sample(s) showing
panels to let users customize their plots.
In the Basic settings
panel, users can select a particular chromosome/sequence
to display after specifying the name of the backbone
sample.
For the start
and end
positions, users can specify both of them, one of them or none. For example,
start
and end
positions, the graph will be limited to the two positions within the selected chromosome/sequence.start
position is given, the program will display a graph between the start
position and the end position of the selected chromosome/sequence.end
position is given, the program will display a graph between 1 to the given end
position within the selected chromosome/sequence.Additionally, the program will check if the given start
and end
positions are qualified automatically. If not, a warning message will pop up and the plot will not be generated.
For the Sample(s) showing
panel, users can select to hide nodes from particular sample(s) if they have such a demand.
After completing the settings above, users can either click the Plot
button in the Plot the Graph
panel to generate the graph or customise the Settings
first and then plot graphs.
In Settings
, users can select Node Shapes
to specify node shapes in either vis.js
-based plot or cytoscape.js
-based plot from the dropdown menus.
Users can also select to use either vis.js
or cytoscape.js
to plot graphs by the number of nodes specified in the Graph Modification
panel under Settings
.
By default, if users want to check graphs with <=200 nodes, vis.js
will be applied to generate graphs. Users can adjust this value (200
) depending on their preference. However, if there are over five thousands
of nodes that users want to browse in one graph, we don't recommend using vis.js
as it may take a long time to load the graph file (an html file).
Depending on the screen/display size, users may also need to adjust the canvas height and width
to make the graph fully show in the canvas if selecting vis.js
-based plot. The hover box may run off the screen if the canvas height and width
settings do not match with users' screen size.
Once all settings are ready, users can click the Plot
button to generate the graphs. After the graph is shown in the display canvas, users can use the mouse
to zoom in and out to check graph details. Users can also move the mouse
close to a specific node to check the node information (mouseover, see the figure below).
From the hover box, users can capture the information, such as
SNP
represents single nucleotide polymorphism, INS
represents insertion, INV
represents inversion, DUP
represents duplication and TRANS
represents translocation.If users decide to use vis.js
to plot graphs, we also provide some options in Settings
to let users customize the plot if they don't like the default one.
graph layout
, edge length
and the degree of node overlapping
.
Users can customise the graph by enabling the options and the corresponding options would be shown in the display canvas during graph display
.
While in cytoscape.js
-based plot, we do not provide such functions or interactions mentioned in the vis.js
-based plot. However, one unique interaction in cytoscape
-based plot is that users can press Ctrl
or command
and hold the left click
button of the mouse
to select particular node regions and then right
click the mouse
to show or hide nodes (see the figure below). This would be useful if users want to check a specific subgraph.
We provide two ways to check the node information.
One way is that users can move the mouse
to a specific node in the display canvas and then a hover box will show the information of the node.
Another way is that users can check the information of nodes from the Available Nodes
panel.
List of the selected node(s)
panel by linesCheck/Plot
button, the program will pop out a diag box asking if users want to browse the sequences of selected nodes or the graph built by the selected nodes. Users can decide by click the corresponding button.Save the Sequences
button to save the fasta
file to the output directory. Users can import the saved sequence file to other programs, such as NCBI-blast
for downstream analyses.Please note that by default we only allow a sequence display with <= 1000000
bp in length. The reason to do this is that if a large sequence is needed to display, it would take a long time to show. Users can change the setting in Settings
--> Graph Modification
if they really want to display a large sequence.
If users have an annotation file for the backbone
sample, they can check gene models that may be interrupted by some sequences in some samples.
Basically, users need to
2
nodes falling in the region can be retained. Users can change this setting in Settings
--> Graph Modification
.After clicking the Plot
button, a plot will show in the display canvas.
Wheel Zoom(x-axis)
button on the right top panel in the canvas.Available Nodes
panel or plot subgraphs
using the coordinate of the gene model.After the installation of the web-based PanGraphViewer, users can follow README
to open it. The login interface is like:
Users can use the test account (demo
) or personal account to open the application.
After opening the page showing above, users can
desktop-based
version, users can upload
and parse
a GFA file, an rGFA
file or a VCF
file to the systemPlot pangenome
panelExtract nodes
panel
Notably, when selecting specific nodes in the graph, the web-based application provides options to directly check/download the node sequence(s).
For the admin
account, users can login using the steps shown in the README
file. The interface of the login page is like:
Once entering the login page, the admin can create accounts for either groups or users.
Enjoy using PanGraphViewer!