valorate (version 1.0-5)

valorate.plot.sampling.densities: PLOT CO-OCCURRENCE DENSITIES FORMING A LOG-RANK DISTRIBUTION

Description

Plots the densities of each co-occurrence that shapes the final log-rank distribution for a n1 group size.

Usage

valorate.plot.sampling.densities(vro, n1, 
  type, log, xlim, ylim, ncol, main, 
  rug, add, w.sum, sampling, 
  weighted,legends.cex, weights.cex,
  weights.pos, w.sum.lwd=3,
  y.limit=1e-13,
  ...)
valorate.plot.sampling.densities.figure(vro, n1, type, log, 
  xlim, ylim, main, rug, rug.size, 
  sub, w.sum, sampling, ncol, 
  y.limit=1e-13, ...)

Value

Nothing.

Arguments

vro

the valorate object.

n1

the size of the 'mutated' or interested survival group. It can be also the numerical/logical 'x' vector as in valorate.survdiff in which case n1 and vstat are estimated.

type

typical plot parameter: "p"=points, "l"=lines (default), "o"=overlap.

log

typical plot parameter : specify which axis are shown in logarithm base 10.

xlim

typical plot parameter.

ylim

typical plot parameter.

ncol

number of columns for legends.

main

typical plot parameter. The default is an expression depending on the parameters.

rug

if FALSE removes the drawing of rugs.

add

if FALSE assumes plots are added to existing one. Not valid for all functions.

w.sum

if FALSE removes the drawing of the weighted sum distribution (the final log-rank distibution).

sampling

if TRUE includes the drawing of a crude-histogram version of the overall distribution (the final log-rank distibution).

weighted

if TRUE the densities of each co-occurrence is weighted to its overall contribution (proportion of combinations). Nice! to explain the overall distribution.

legends.cex

the character expansion for legends.

weights.cex

the character expansion for legends of the weights

weights.pos

the position of the weights "middle"=above each curve, "left", or "right".

w.sum.lwd

the line width of the weighted sum line.

...

parameters forwarded to plot.

rug.size

determine the size of rugs made in valorate.plot.sampling.densities.figure

sub

specifies the character to include in each plot.

y.limit

specifies the lowest density value. The default is 1e-13. This is useful for log="y".

Author

Victor Trevino

Details

Plots the densities of each co-occurrence that shapes the final log-rank distribution for a n1 group size. valorate.plot.sampling.densities plots all co-occurrences in the same figure whereas valorate.plot.sampling.densities.figure plots all in separated figures.

References

Trevino et al. 2016 https://bioinformatics.mx/index.php/bioinfo-tools/

See Also

new.valorate. valorate.survdiff.

Examples

## Create a random population of 100 subjects 
## having 20 events
subjects <- numeric(100)
subjects[sample(100,20)] <- 1
vo <- new.valorate(rank=subjects, sampling.size=100000, verbose=TRUE)

if (FALSE) valorate.plot.sampling.densities(vo, 5)
if (FALSE) valorate.plot.sampling.densities(vo, 10)
if (FALSE) valorate.plot.sampling.densities(vo, 20, weighted=TRUE)

if (FALSE) valorate.plot.sampling.densities.figure(vo, 5)