plot_order: Plots ordered datasets

In asael697/fdaRNA: RNA-Seq and Microarray Preprocessing

Description

In the process of normalization, statistical depth based or quantile, each element of the sample is ordered in ascending order. This function plots the sample elements in this process.

Usage

plot_order(
  ar,
  x = 1:nrow(ar),
  tp = "l",
  xl = range(x),
  yl = c(min(ar[x, ]), max(ar[x, ])),
  xlb = "",
  ylb = "",
  m = "",
  ...
)

Arguments

ar	Cell files from Affy micrarray experiment: a matrix where the columns are the sample elements, RNA-seq or microarray, and the rows the variables (the genes).
x	A vector that is subset of the natural numbers up to the number of variables. It represents the domain, of the X-axis, to use for the zoomed plot. The default is the whole domain.
tp	The type of plot that should be drawn. The default is "l" for lines.
xl	A vector with the limits of the X-axis. The default is the range of "x".
yl	A vector with the limits of the Y-axis. The default is the range of "ar" when restricted to the domain "x".
xlb	X-axis label for the multidimensional scaling and/or spectral map plots. The default is empty. It is only used if "MS" or/and "SM" is/are set to TRUE.
ylb	Y-axis label for the multidimensional scaling and/or spectral map plots. The default is empty. It is only used if "MS" or/and "SM" is/are set to TRUE.
m	Main title plot. The default is empty
...	Additional arguments to be passed to the multidimensional scaling and/or spectral map plots, such as graphical parameters. It is only used if "MS" or/and "SM" is/are set to TRUE.

Details

This function plots allows to plot a zoom of the domain. The color shows the deepness of the sample elemnt with respect to the sample, using prof.funct. The colours go from blue meaning low depth to red meaning high depth, through green and yellow.

Value

does not return

Author(s)

Alicia Nieto-Reyes and Javier Cabrera

References

Nieto-Reyes A, Cabrera J. Statistical depth based normalization and outlier detection of gene expression data. Preprint.

See Also

normalization and prof.funct

Examples

# Plots the Sialin data set after 6 hours of gestation, in the ascending order used 
# in the process of normalization
plot_order(Sialin6)

# A zoom of previous plot in the interval [20000 , 30000]
plot_order(Sialin6, c(20000:30000))

asael697/fdaRNA documentation built on May 28, 2020, 11:32 a.m.