Function to plot the uncertainty in the loading in the conformational landscape. Typically used to obtain uncertainty in the conformational signatures.

Function to plot the uncertainty in the loading in the conformational landscape. Typically used to obtain uncertainty in the conformational signatures.

plotTREuncertaintyLoadings(
  df_all,
  pca_states,
  states,
  whichSamples = seq.int(1, 50)
)

Arguments

df_all

The data frame containing the TRE values and the residue number over monte carlo interations. Results from the sampleTREuncertainty function.

pca_states

The PCA object from the UnsupervisedCSA function

states

The state name to use for the analysis. e.g. ligand used in differential analysis

whichSamples

The samples to use for the analysis. Default is seq.int(1, 50)

Value

A ggplot object

Examples

library("RexMS")
data(TRE_dist)
data("out_lxr_compound_proccessed")
data("LXRalpha_compounds")

states <- names(LXRalpha_compounds)

ucsa <- UnsupervisedCSA(out_lxr_compound_proccessed,
                       quantity = "TRE",
                       states = states,
                       whichTimepoint = 600,
                       pca_params = list(scale = FALSE,
                                         center = TRUE))
                       

plotTREuncertaintyLoadings(df_all = TRE_dist,
                          pca_states = ucsa$pca_states,
                          states = states,
                          whichSamples = seq.int(1, 50))