Plot Summary Scores as Histograms

This function generates a ggplot object.

Usage

histogramRndSigScores(
  rndata,
  data = NULL,
  obs,
  score,
  hist.colour = "black",
  hist.fill = "white",
  bins = 30,
  vline.colour = "darkred",
  vline.linetype = "dashed",
  vline.linewidth = 1,
  labs.title = "Diagnostic Plot",
  labs.x = "Summary Score",
  labs.y = "Count",
  ...
)

Arguments

rndata

data frame, output of computeSigScores containing random scores.

data

(optional) data frame, output of computeSigScores.

obs

character string, indicating the sample to plot from rndata and data.

score

character string, indicating the score to plot from rndata and data.

hist.colour, hist.fill

character strings, aesthetics parameters indicating the colors used to draw the contours and the inside areas of the histogram bars. See also geom_histogram.

bins

integer, number of bins.

vline.colour, vline.linetype, vline.linewidth

character strings, indicating the color, type, and width of the vertical line. See also geom_vline

labs.title

The text for the plot title.

labs.x

The title of the x axis.

labs.y

The title of the y axis.

...

further arguments to geom_histogram.

Value

A ggplot object.

See also

geom_histogram

Author

Alessandro Barberis

Examples

#Set seed for reproducibility
set.seed(seed = 5381L)

#Define signature size
nsig = 8

#Define row/col size
nr = nsig + 50
nc = 10

#Create input matrix
x = matrix(
 data = c(
    stats::runif(n = nsig*nc, min = 500, max = 1000),
    stats::runif(n = (nr-nsig)*nc, min = 0, max = 700)
 ),
 nrow = nr,
 ncol = nc,
 dimnames = list(
    paste0("g",seq(nr)),
    paste0("S",seq(nc))
 ),
 byrow = TRUE
)

#Define signature
sig = rownames(x)[1:nsig]

#Compute Summary Scores
scores = computeSigScores(
 x = x,
 i = sig
)

#Compute Random Summary Scores
rndscores = computeSigScores(
 x = x,
 i = sig,
 sampling = "bootstrap",
 n.repeat = 100
)

#Plot null distribution
histogramRndSigScores(
 rndata = rndscores,
 data = scores,
 obs = "S1",
 score = "sum"
)