View source: R/visualization.R
netVisual_chord_cell_internal | R Documentation |
Names of cell states/groups will be displayed in this chord diagram
netVisual_chord_cell_internal(
net,
color.use = NULL,
group = NULL,
cell.order = NULL,
sources.use = NULL,
targets.use = NULL,
lab.cex = 0.8,
small.gap = 1,
big.gap = 10,
annotationTrackHeight = c(0.03),
remove.isolate = FALSE,
link.visible = TRUE,
scale = FALSE,
directional = 1,
link.target.prop = TRUE,
reduce = -1,
transparency = 0.4,
link.border = NA,
title.name = NULL,
show.legend = FALSE,
legend.pos.x = 20,
legend.pos.y = 20,
...
)
net |
a weighted matrix or a data frame with three columns defining the cell-cell communication network |
color.use |
colors for the cell groups |
group |
A named group labels for making multiple-group Chord diagrams. The sector names should be used as the names in the vector. The order of group controls the sector orders and if group is set as a factor, the order of levels controls the order of groups. |
cell.order |
a char vector defining the cell type orders (sector orders) |
sources.use |
a vector giving the index or the name of source cell groups |
targets.use |
a vector giving the index or the name of target cell groups. |
lab.cex |
font size for the text |
small.gap |
Small gap between sectors. |
big.gap |
Gap between the different sets of sectors, which are defined in the 'group' parameter |
annotationTrackHeight |
annotationTrack Height |
remove.isolate |
whether remove sectors without any links |
link.visible |
whether plot the link. The value is logical, if it is set to FALSE, the corresponding link will not plotted, but the space is still ocuppied. The format is a matrix with names or a data frame with three columns |
scale |
scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE |
directional |
Whether links have directions. 1 means the direction is from the first column in df to the second column, -1 is the reverse, 0 is no direction, and 2 for two directional. |
link.target.prop |
If the Chord diagram is directional, for each source sector, whether to draw bars that shows the proportion of target sectors. |
reduce |
if the ratio of the width of certain grid compared to the whole circle is less than this value, the grid is removed on the plot. Set it to value less than zero if you want to keep all tiny grid. |
transparency |
Transparency of link colors |
link.border |
border for links, single scalar or a matrix with names or a data frame with three columns |
title.name |
title name of the plot |
show.legend |
whether show the figure legend |
legend.pos.x, legend.pos.y |
adjust the legend position |
... |
other parameters passing to chordDiagram |
an object of class "recordedplot"
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.