iCheck (version 1.2.0)

plotSamplep95p05: Plot trajectories of the ratio of 95th percentile to 5th percentile of sample probe profiles across arrays

Description

Plot trajectories of the ratio of 95th percentile to 5th percentile of sample probe profiles across arrays.

Usage

plotSamplep95p05( es,  labelVariable = "subjID",  hybName = "Hybridization_Name", requireLog2 = FALSE,  projectName = "test",  plotOutPutFlag = FALSE,  cex = 1,  ylim = NULL,  xlab = "",  ylab = "",  lwd = 1.5,  mar = c(10, 4, 4, 2) + 0.1,  las = 2,  cex.axis=1.5, title = "Trajectory of p95/p05", cex.legend = 1.5, cex.lab = 1.5, legendPosition = "topright", cut1 = 10, cut2 = 6, sortFlag = TRUE, varSort = c("Batch_Run_Date", "Chip_Barcode", "Chip_Address"),  timeFormat = c("%m/%d/%Y", NA, NA), verbose = FALSE, ...)

Arguments

es

ExpressionSet object of Sample probe profiles.

labelVariable

A character string. The name of a phenotype data variable use to label the arrays in the boxplots. By default, labelVariable = "subjID" which is equivalent to labelVariable = "Hybridization_Name".

hybName

character string. indicating the phenotype variable Hybridization_Name.

requireLog2

logical. requiredLog2=TRUE indicates probe expression levels will be log2 transformed. Otherwise, no transformation will be performed.

projectName

A character string. Name of the project. The plots will be saved as pdf format files, the names of which have the format projectName_probeName_traj_plot.pdf.

plotOutPutFlag

logical. plotOutPutFlag=TRUE indicates the plots will be output to pdf format files. Otherwise, the plots will not be output to external files.

cex

numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. see par.

ylim

Range of y axis.

xlab

Label of x axis.

ylab

Label of y axis.

lwd

The line width, a _positive_ number, defaulting to '1'. see par.

mar

A numerical vector of the form 'c(bottom, left, top, right)' which gives the number of lines of margin to be specified on the four sides of the plot. The default is 'c(5, 4, 4, 2) + 0.1'. see par.

las

'las' numeric in 0,1,2,3; the style of axis labels. 0 - always parallel to the axis, 1 - always horizontal, 2 - always perpendicular to the axis, or 3 - always vertical.

see par.

cex.axis

The magnification to be used for axis annotation relative to the current setting of cex.

see par.

title

Figure title.

cex.legend

Font size of legend text.

cex.lab

The magnification to be used for x and y labels relative to the current setting of cex.

legendPosition

Position of legend. Possible values are “bottomright”, “bottom”, “bottomleft”, “left”, “topleft”, “top”, “topright”, “right” and “center”.

cut1

second horiztonal line setting the cutoff for the ratio p95/p05. A ratio above this line indicates the corresponding array is good.

cut2

second horiztonal line setting the cutoff for the ratio p95/p05. A ratio below this line indicates the corresponding array is bad.

sortFlag

logical. Indicates if arrays need to be sorted according to Batch_Run_Date, Chip_Barcode, and Chip_Address.

varSort

A vector of phenotype variable names to be used to sort the samples of es.

timeFormat

A vector of time format for the possible time variables in varSort. The length of timeFormat should be the same as that of varSort. For non-time variable, the corresponding time format should be set to be equal to NA. The details of the time format for time variable can be found in the R function strptime.

verbose

logical. Determine if intermediate output need to be suppressed. By default verbose=FALSE, intermediate output will not be printed.

...

Arguments to be passed to plot.

Value

A list of 2 elements. The first element is the 2 x n matrix, where n is the number of arrays. The first row of the matrix is the 5-th percentile and the second row of the matrix is the 95-th percentile.The second element is the ratio of the 95-th percentile to the 5-th percentile.

Details

The trajectory of the ratio of 95 to 5

Examples

    # generate simulated data set from conditional normal distribution
    set.seed(1234567)
    es.sim = genSimData.BayesNormal(nCpGs = 100, 
      nCases = 20, nControls = 20,
      mu.n = -2, mu.c = 2,
      d0 = 20, s02 = 0.64, s02.c = 1.5, testPara = "var",
      outlierFlag = FALSE, 
      eps = 1.0e-3, applier = lapply) 
    print(es.sim)

  es.sim$Batch_Run_Date = 1:ncol(es.sim)
  es.sim$Chip_Barcode = 1:ncol(es.sim)
  es.sim$Chip_Address = 1:ncol(es.sim)
  

 plotSamplep95p05(
  es = es.sim, 
  labelVariable = "subjID", 
  hybName = "memSubj",
  requireLog2 = FALSE, 
  projectName = "test", 
  plotOutPutFlag = FALSE, 
  title = "Trajectory of p95/p05",
  cex.legend = 0.5,
  legendPosition = "topright",
  sortFlag = TRUE,
  varSort = c("Batch_Run_Date", "Chip_Barcode", "Chip_Address"), 
  timeFormat = c("%m/%d/%Y", NA, NA),
  verbose = FALSE)