plotChordDiagram: plotChordDiagram Generate a chord diagram from a flowReMix...

In RGLab/flowReMix: Generalized Linear Modeling of FCM Data With Clustered Coefficients

Description

plotChordDiagram Generate a chord diagram from a flowReMix fit.

Usage

plotChordDiagram(x, threshold = 0.6, varnames = c("stim", "parent",
  "functions"), separator = "/", function.separator = "\\+",
  track.order = c("functions", "parent", "stim"),
  sort.order = c("functions", "parent", "stim"), inner.track = "parent",
  track.height = 2, track.margin = c(0, 0), functions.name = "functions",
  wrap.at = c("\\+", "", ""), label.cex = c(0.5, 0.5, 0.5),
  facing = "clockwise", parsefun = NULL, functionality.filter = NULL,
  auc.filter = NULL, auc.outcome = NULL, response.filter = NULL)

Arguments

x	flowReMix fit
threshold	numeric threshold for the minimum edge weight in the graph (exclusive).
varnames	character variable names to define by splitting subsets. e.g. c("parent","stim","function")
separator	character separator to split subset string into variables.
function.separator	character separator to split multifunction string into individual functions.
track.order	character vector of the same length as varnames specifying the order of the variables in the tracks.
sort.order	character vector of the same length as varnames specifying the order of the variables in the tracks.
inner.track	character specifying which variable in varnames is on the inner track.
track.height	numeric vector of track heights, length 1 or length(varnames)
track.margin	numeric vector of length 2 specifying the track margin.
functions.name	character length 1, name of the column holding the functions.
wrap.at	character regex, string position to wrap labels for all tracks.
label.cex	numeric scaling factors for the labels in each track.Should be same length as varnames.
facing	character passed to circos.text. facing=c("inside", "outside", "reverse.clockwise", "clockwise", "downward", "bending", "bending.inside", "bending.outside")
parsefun	function that parses multiple function labels to single function matrix.
functionality.filter	numeric lower threshold for functionality degree. Exclusive.
auc.filter	numeric lower threshold for AUC prediction. Exclusive.
auc.outcome	name unquoted variable name used for prediction to calculate the AUC.
response.filter	numeric minimum cell subset response probability to include.

Details

Parses the subsets labels into factors that can be used to annotate tracks on a chord diagram. Connections correspond to edges in the ising stability graph with a minumum threshold propensity. A label such as "env/8+/IL2+" with an argument of separator="/" and varnames=c("stim","parent","functions") would cause the cell subset label to be parsed into three variables corresponding to the stimulation, the parent cell population, and the cytokine function.

Examples

data(fit505)
#also defined in the package namespace
parser = function(x,separator,functions){
  functions=enquo(functions)
   dat = x%>% mutate(func = strsplit(!!functions, split = separator)) %>%
  unnest()%>%tidyr::spread(func,func)
 dat[is.na(dat)]=""
 dat
}
plotChordDiagram(fit505,
   threshold = 0.8,
   varnames=c("stim","parent","functions"),
   track.order = c("stim","parent","functions"),
   sort.order=c("parent","stim","degree"),
   functions.name="functions",
   track.height = 2.5,
   track.margin = c(0,0),
   label.cex=0.6,
   wrap.at = " ",
   functionality.filter=1,
   auc.filter = 0,
   auc.outcome = hiv,
   response.filter = 0.05,
   facing=c("inside","inside","inside"),parsefun=parser)
   ## Not run: 
   plotChordDiagram(
     rv144_aggregate,
     threshold = 0.8,
     varnames = c("functions"),
     separator = " ",
     function.separator = ",",
     track.order = "functions",
     sort.order = c("degree", "functions"),
     inner.track = "functions",
     parsefun = parser,
     track.height = 2,
     track.margin = c(0, 0),
     functions.name = c("functions"),
     facing = "inside",
     wrap.at = " ",
     label.cex = 0.6,
     functionality.filter=1
)
   
## End(Not run)

RGLab/flowReMix documentation built on May 8, 2019, 5:55 a.m.