Drag&drop
one or more files to the network panel, or load the file(s) using the menu File-->Open.... The files can be any formats supported by the platform, including MIND data JSON format, as well as MIND worksapce JSON format that stores all the information of the workspace.
double-clicking
will alos query its interactions.
enter
or ,
to complete the name/ID.
context
can be loaded by click the All button of the correspondingcontext
in the Toolbox panel.
mouse wheel
to zoom in/out the network, or you may click the +/- button on the Toolbox (left side) to achieve the same operation.
mouse with the right mouse key
(press the right mouse key
down and drag the mouse
) to move the network around.
the left mouse-clicking
to make single node selection.Left mouse dragging
over the area of interested nodes to make the selection. CTRL
key and use left mouse-clicking
to add/remove a node to the selections
size
and color
of the nodes, as well as the size
and color
of the node label, can be changed under the Options tag. Select the checkbox Label, or use the menu Nodes-->Label to turn on the label of selected nodes.
color
is determined by its taxonomy ranking, which can be changed by clicking the color button of the corresponding ranking in the Toolbox panel.
color
of the node label is same as the as the one of the node.
color
of the edges is determined by the context
of the network, which can be changed by clicking the color button of the corresponding context
in the Toolbox panel.
tooltips
of nodes and edges when mouse-over
them.labels
of all nodes.edge opacity
can be changed by the field Edge Opacity under the tag Optionsedge thickness
can be changed by the field Edge Thickness under the tag Optionsnode opacity
can be changed by the field Node Opacity under the tag Optionsalpha
can be changed under Options tag. The layout will apply the change if force layout is running.
raxonomy ranking
, uncheck the checkbox for each ranking will hide corresponding nodes.
context
-specific weight cutoff, which can be found in the line for the corresponding context
.
contexts
, just uncheck the checkbox
in the line of each context
will be invisible.
A context
in MIND database basically is the combination of the network with its associated meta data. The context panel in the Toolbox list all contexts
that are available in MIND database. In addition, when users load their own networks, the corresponding contexts
will also available there. Follwing are the filters to help to find specific contexts:
conditions
. For Human microbiome, the condition
points to the health state
.
contexts
based on the type of interactions
, e.g., co-occurrence correlation
etc.
contexts
based on the location
where microbes live.
Carts
can be used to store your pick of contexts
. If a user is logged in, the contexts
picked by the user will be stored on-line.
contexts
only involved in the current network, which can be achieved through the menu Filters --> Show only contexts in the current network.
NCBI taxonomy ID
as the primary key for microbes while OTU
(operational taxonomic unit) are often used in microbial studies, resulting many different OTUs
being mapped to the same taxonomy ID
. Therefore it is often that there are many links between a given pair of microbes even under the same context
. By default, these links are merged with their weight averaged. This can be changed in the Edge merging field under Options tag.
context
may be associated with an abundance
profile. By default the adundance button associated with the context
is disabled. It will be enabled as if the adundance of the context is available. Click
the button will map the node size to its abundance value, and the button will be changed to
node degree
(the number of links of the node) can be mapped to it size using the menu Edit-->Map Node Size to Its Degree.
Abundance
mapping has higher priority than the degree
mapping.
contexts
stored in the cart
will be saved in the server.
context
is loaded in MIND-web by the user, the button associated with the the context
will be replace by the upload button , and only the login user can submit the context
to MIND server.