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.
Details
The trajectory of the ratio of 95
to 5
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.
Author(s)
Weiliang Qiu <stwxq@channing.harvard.edu>,
Brandon Guo <brandowonder@gmail.com>,
Christopher Anderson <christopheranderson84@gmail.com>,
Barbara Klanderman <BKLANDERMAN@partners.org>,
Vincent Carey <stvjc@channing.harvard.edu>,
Benjamin Raby <rebar@channing.harvard.edu>