boxplotPhi: Draws a boxplot of the phi distribution for all exons/groups.

Description Usage Arguments Details See Also

Description

Draws a boxplot of the posterior phi distributions for all exons within a transcript. Can be either a contrast (phiLogFC) or a parameter (phi).

Usage

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boxplotPhi(data, unit, which = 1, maxB = log(6001),
  bThresh = log(2997.5/3.5), nProbes, grpNames, featName = NULL,
  showGroups = TRUE, unchCol = "white", upCol = "green",
  downCol = "red", ..., widths, main = NULL, medLwd = 2, lty = 1,
  las = 2, cex.x = 0.9, cex.y = 0.9, h = 0, abCol = "blue",
  hLab = "*", col.axis = c("black", "grey"))

Arguments

data

can be either an array, matrix or AffymetrixCelSetList

unit

specifies which unit to plot if data is an AffymetrixCelSetList. Ignored if data is an array or matrix.

which

specifies which condition/cell-type or contrast to plot. Defaults to the first condition or contrast

maxB

the maximum possible B-statistic from the entire dataset. Should be log(2*(nChains*(nIter-nBurnin))/nThin+1) from the mcmcParam object in the general workspace. Only used if plotting a contrast.

bThresh

the maximum B-statistic to display in colour

nProbes

the number of probes per group. Will over-ride any values found on an associated AffymetrixCdfFile for a given unit

grpNames

the names of the group-level probesets. Will over-ride any found on an AffymetrixCdfFile

featName

the feature being plotted. Should be a cell-type/condition if plotting raw phi values, or the contrast name if plotting a contrast. Not required if extracting data from an AffymetrixCelSetList

showGroups

logical. Determines whether to diplay the groupNames on the x-axis.

unchCol

the default fill colour for the boxplots

upCol

the colour to use for contrast values greater than bThresh

downCol

the colour to use for contrast values less than -bThresh

...

passes any further specified graphical parameters

widths

the width of the boxes. Over-rides any values calculated from an AffymetrixCdfFile

main

the title of the plot

medLwd

the width of the line to draw for the medians

lty

the line-type for the whiskers

las

see plot

cex.x

cex.axis for the x-axis labels

cex.y

cex.axis for the y-axis labels

h

values at which a horizontal line will be drawn

abCol

the colour of any horizontal-lines

hLab

text characters to denote significantly up/down changed groups

col.axis

the colour for the main axes & any zero line

Details

Plots the posterior distributions for the exon proportions (phi) as specified by the BMEA model. Either the distributions for a given cell type, or a given contrast will be plotted.

Whiskers will extend from the 75th to 97.5th quantile and from the 25th to the 2.5th quantile. The box will display the IQR.

In the case of a contrast, any significant groups will be indicated by default with an asterisk. These will only appear for groups with a B-statistic equal to the maximum possible value. Groups with B-statistics less than this value, but above the specified value for bThresh will be coloured using upCol or downCol.

See Also

AffymetrixCelSetList, AffymetrixCdfFile, boxplot


steveped/BMEA documentation built on May 30, 2019, 5:38 p.m.