foldChangeArrow2: Add arrow for expected Fold-Change to VolcanoPlot or MA-plot

In wrProteo: Proteomics Data Analysis Functions

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

Description

NOTE : This function is deprecated, please use foldChangeArrow instead !! This function was made for 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

foldChangeArrow2(
  FC,
  useComp = 1,
  isLin = TRUE,
  asX = TRUE,
  col = 1,
  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) display additional messages for debugging
callFrom	(character) allow easier tracking of message(s) produced

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.

Ultimately this function will be integated to the package wrGraph.

Value

plots arrow only (and explicative text), if returnRatio=TRUE also returns numeric value for extracted ratio

See Also

new version : foldChangeArrow; used with MAplotW, VolcanoPlotW

Examples

plot(rnorm(20,1.5,0.1),1:20)
#deprecated# foldChangeArrow2(FC=1.5) 

wrProteo documentation built on April 12, 2025, 1:16 a.m.