Function to plot the uncertainty in the TRE values for different states e.g. ligands. Typically used to obtain uncertainty in the conformational landscape.

Function to plot the uncertainty in the TRE values for different states e.g. ligands. Typically used to obtain uncertainty in the conformational landscape.

plotTREuncertainty(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))
                       
                       
plotTREuncertainty(df_all = TRE_dist,
                  pca_states = ucsa$pca_states,
                  states = states,
                  whichSamples = seq.int(1, 50))
#> Warning: Duplicated aesthetics after name standardisation: contour
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: `stat_contour()`: Zero contours were generated
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf