gate {prada} | R Documentation |
These functions allow the user to select a number of observations in
multivariate data by circling them in two-dimensional projections of
the data. gate.cytoSet
calls gate.cytoFrame
seperately
on each frame in the set. gate.matrix
does the same as
gate.cytoSet
but only requires a data matrix.
my.gate <- gate.cytoFrame(object, gate.colour = "red", use.smoothScatter = FALSE, data.min = 0, data.max = 1023, max.observations = 20000)
object |
cytoFrame , cytoSet or matrix of cytometry
data, from which observations are to be selected by gating |
gate.colour |
colour of the drawn polygons |
use.smoothScatter |
logical, should the function
smoothScatter be employed for plotting the data
(plots data densities rather than individual points) |
data.min |
minimum value to (theoretically occur in the data; e.g. with 10-channel-digitized data, it is 0 |
data.max |
minimum value to (theoretically occur in the data; e.g. with 10-channel-digitized data, it is 1023 |
max.observations |
maximum number of observations from the data to be plotted; large values decrease performance |
The user is prompted to select the two dimensions for the projection and the defines a polygon by left-mouse clicks on its vertices. To finish drawing the polygon, press the right mouse button. Observations within the polygon are computed and marked. The user is then prompted if he wants to
For gate.cytoFrame
and gate.matrix
, it is a logical
vector stating for each observation in the data (in same order) wether
it was included in the defined gate (TRUE
) or not
(FALSE
). For gate.cytoSet
, it is a list of logical
vectors, one for each cytoFrame
in the cytoSet
.
The class of the result depends on the called function and is
cytoFrameGate
,cytoSetGate
, or matrixGate
.
Joern Toedling toedling@ebi.ac.uk
Classes cytoFrame-class
,
cytoSet-class
, plot.cytoFrameGate
for
plotting
## Not run: # don't run during package test, because requires user input # read in FCS files: mySet <- readCytoSet(...) # let user do gating: mySGate <- gate.cytoSet(mySet) # visualize gating: plot(mySGate,mySet,pch=".",cex=2) ## End(Not run)