flatPlot {twoddpcr} | R Documentation |
There are occasions where classification algorithms fail for various reasons (such as poor choice/number of centres in k-means clustering). In these cases, it may be helpful to the user if an app draws a 'flat' plot with just one colour rather than nothing at all.
If a ddpcrWell
object is given as a parameter, plot the
droplets in the well and colour them according to a given class.
If a ddpcrPlate
object is given as a parameter,
plot the droplets in all wells and colour them according to a given class.
flatPlot(droplets, ch1Label = "Ch1 Amplitude", ch2Label = "Ch2 Amplitude", classString = ddpcr$na, initialCentres = NULL, selectedCentre = NULL, plotLimits = list(x = c(1000, 9000), y = c(3000, 13500))) ## S4 method for signature 'data.frame' flatPlot(droplets, ch1Label = "Ch1 Amplitude", ch2Label = "Ch2 Amplitude", classString = ddpcr$na, initialCentres = NULL, selectedCentre = NULL, plotLimits = list(x = c(1000, 9000), y = c(3000, 13500))) ## S4 method for signature 'ddpcrWell' flatPlot(droplets, ch1Label = "Ch1 Amplitude", ch2Label = "Ch2 Amplitude", classString = ddpcr$na, initialCentres = NULL, selectedCentre = NULL, plotLimits = list(x = c(1000, 9000), y = c(3000, 13500))) ## S4 method for signature 'ddpcrPlate' flatPlot(droplets, ch1Label = "Ch1 Amplitude", ch2Label = "Ch2 Amplitude", classString = ddpcr$na, initialCentres = NULL, selectedCentre = NULL, plotLimits = list(x = c(1000, 9000), y = c(3000, 13500)))
droplets |
A data frame of droplet amplitudes, or
a |
ch1Label |
The label for the channel 1 target. Defaults to "Ch1 Amplitude". |
ch2Label |
The label for the channel 2 target. Defaults to "Ch2 Amplitude". |
classString |
The class that all droplets should be classified as.
Defaults to the |
initialCentres |
A data frame of initial centres to plot (e.g. initial
cluster centres used in the k-means). This is _not_ restricted to the class
|
selectedCentre |
An initial centre to highlight. This should be either
"NN", "PN", "NP" or "PP", but is _not_ restricted to the class 'classString'
only. If |
plotLimits |
A list of 2-element vectors with names |
A ggplot object in just one colour corresponding to
classString
.
Anthony Chiu, anthony.chiu@cruk.manchester.ac.uk
## Plot the data frame with no classification. aWell <- KRASdata[["E03"]] flatPlot(aWell) ## Take a ddpcrWell object that is mostly classified as "NN" and colour it ## as such. aWell <- KRASdata[["H04"]] emptiedWell <- aWell[aWell$Cluster == 1, ] emptiedWell <- ddpcrWell(well=emptiedWell) flatPlot(emptiedWell, classString="NN") ## Plotting all of a ddpcrPlate object works the same way. krasPlate <- ddpcrPlate(wells=KRASdata) flatPlot(krasPlate)