chord_diagram {barcodetrackR} | R Documentation |
Creates a chord diagram showing each cell type (or other factor) as a region around a circle and shared clones between these cell types as links between the regions. The space around the regions which is not connected to a chord indicates clones unique to that sample, not shared with other samples.
chord_diagram( your_SE, weighted = FALSE, plot_label = "SAMPLENAME", alpha = 1, your_title = NULL, text_size = 12, return_table = FALSE )
your_SE |
Summarized Experiment object containing clonal tracking data as created by the barcodetrackR 'create_SE' function. |
weighted |
Logical. weighted = F which is default will make links based on the number of shared clones between the factors. Weighted = TRUE will make the link width based on the clone's proportion in the samples. |
plot_label |
Character. Name of colData variable to use as labels for regions. Defaults to SAMPLENAME |
alpha |
Numeric. Transparency of links. Default = 1 is opaque. 0 is completely transluscent |
your_title |
Character. The title for the plot. |
text_size |
Numeric. Size of region labels |
return_table |
Logical. If set to TRUE, in addition to plotting a chord diagram in the plot window, the function will return a dataframe of the shared clonality used to make the chord diagram. If Weighted is FALSE, the dataframe will contain a row for each set of clones and values of 1 or 0 indicating the samples which share that set of clones, and a freq column which is the number of clones in that set. If weighted is set to TRUE, each row will contain a set of clones and the data will show the proportion that set of clones comprises in each sample. The proportions of 0 indicate which samples do not share that set of clones. |
Displays a chord diagram in the current plot window depicting shared clonality between samples (regions) as chords or links between the regions. Or,
data(wu_subset) chord_diagram(your_SE = wu_subset[, c(4, 8, 12)], plot_label = "celltype")