foldChangeArrow2 {wrProteo} | R Documentation |
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 |
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 |
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)