foldChangeArrow: Add arrow for expected Fold-Change to VolcanoPlot or MA-plot

In wrGraph: Graphics in the Context of Analyzing High-Throughput Data

Add arrow for expected Fold-Change to VolcanoPlot or MA-plot

Description

This function allows adding an arrow indicating a fold-change to MA- or Volcano-plots. When comparing mutiple concentratios of standards in benchmark-tests it may be useful to indicate the expected ratio in a pair-wise comparison. In case of main input as list or MArrayLM-object (as generated from limma), the colum-names of multiple pairwise comparisons can be used for extracting a numeric content (supposed as concentrations in sample-names) which will be used to determine the expected ratio used for plotting. Optionally the ratio used for plotting can be returned as numeric value.

Usage

foldChangeArrow(
  FC,
  useComp = 1,
  isLin = TRUE,
  asX = TRUE,
  col = 2,
  arr = c(0.005, 0.15),
  lwd = NULL,
  addText = c(line = -0.9, cex = 0.7, txt = "expected", loc = "toright"),
  returnRatio = FALSE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

FC	(numeric, list or MArrayLM-object) main information for drawing arrow : either numeric value for fold-change/log2-ratio of object to search for colnames of statistical testing for extracting numeric part
useComp	(integer) only used in case FC is list or MArrayLM-object an has multiple pairwise-comparisons
isLin	(logical) inidicate if FC is log2 or not
asX	(logical) indicate if arrow should be on x-axis
col	(integer or character) custom color
arr	(numeric, length=2) start- and end-points of arrow (as relative to entire plot)
lwd	(numeric) line-width of arrow
addText	(logical or named vector) indicate if text explaining arrow should be displayed, use TRUE for default (on top right of plot), or any combination of 'loc','line','cex','side','adj','col','text' (or 'txt') for customizing specific elements
returnRatio	(logical) return ratio
silent	(logical) suppress messages
debug	(logical) additonal messages for debugging
callFrom	(character) allows easier tracking of messages produced

Details

#' @details The argument addText also allows specifying a fixed position when using addText=c(loc="bottomleft"), also bottomright, topleft, topright, toleft and toright may be used. In this case the elemts side and adjust will be redefined to accomodate the text in the corner specified.

Value

This function plots only an arrow onto current plotting device (and some explicative text), if returnRatio=TRUE also returns numeric value for extracted ratio

See Also

MAplotW, VolcanoPlotW

Examples

plot(rnorm(20,1.5,0.1), 1:20)
foldChangeArrow(FC=1.5) 

wrGraph documentation built on Oct. 20, 2023, 5:08 p.m.