plotRespFun {RCM} | R Documentation |
Plots a number of response functions over the observed range of the environmental score. If no taxa are provided those who react most strongly to the environmental score are chosen.
plotRespFun(RCM, taxa = NULL, type = "link", logTransformYAxis = FALSE, addSamples = TRUE, samSize = NULL, Dim = 1L, nPoints = 100L, labSize = 2.5, yLocVar = NULL, yLocSam = NULL, Palette = "Set3", addJitter = FALSE, nTaxa = 9L, angle = 90, legendLabSize = 15, legendTitleSize = 16, axisLabSize = 14, axisTitleSize = 16, lineSize = 0.75, ...)
RCM |
an RCM object |
taxa |
a character vector of taxa to be plotted |
type |
a character string, plot the response function on the log-scale ('link') or the abundance scale 'response', similar to predict.glm(). |
logTransformYAxis |
a boolean, should y-axis be log transformed? |
addSamples |
a boolean, should sample points be shown? |
samSize |
a sample variable name or a vector of length equal to the number of samples, for the sample sizes |
Dim |
An integer, the dimension to be plotted |
nPoints |
the number of points to be used to plot the lines |
labSize |
the label size for the variables |
yLocVar |
the y-location of the variables, recycled if necessary |
yLocSam |
the y-location of the samples, recycled if necessary |
Palette |
which color palette to use |
addJitter |
A boolean, should variable names be jittered to make them more readable |
nTaxa |
an integer, number of taxa to plot |
angle |
angle at which variable labels should be turned |
legendLabSize |
size of the legend labels |
legendTitleSize |
size of the legend title |
axisLabSize |
size of the axis labels |
axisTitleSize |
size of the axis title |
lineSize |
size of the response function lines |
... |
Other argumens passed on to the ggplot() function |
Plots a ggplot2-object to output
data(Zeller) require(phyloseq) tmpPhy = prune_taxa(taxa_names(Zeller)[1:100], prune_samples(sample_names(Zeller)[1:50], Zeller)) #Subset for a quick fit zellerRCMnp = RCM(tmpPhy, k = 2, covariates = c('BMI','Age','Country','Diagnosis','Gender'), round = TRUE, responseFun = 'nonparametric') plotRespFun(zellerRCMnp)