staggerdCountsPlot {wrGraph} | R Documentation |
Staggered Chart for Ploting Counts to Multiple Leveles of the Threshold used
Description
The basic idea of this plot is to show how counts data change while shifting a threshold-criterium.
At each given threshold the counts are plotted like a staggered bar-chart (or staggered histogram) but without vertical lines to illustrated the almost continuous change
from preceedig or following threshold-value.
Initially this plot was designed for showing the absolute count-data used when constructing roc-curves (eg using
the function summarizeForROC
of package wrProteo ).
The main input should furnish the panel of threshold as one column and the coresponding counts data as min 2 columns.
The threshold coumns gets specified using the argument threColumn
, the counts-data may either be specified using argument countsCol
or be searched using grep
using column-names containing the text given in argument varCountNa
with may be combined with
a fixed preceeding part given as argument fixedCountPat
.
Usage
staggerdCountsPlot(
roc,
threColumn = 1,
countsCol = NULL,
fixedCountPat = "n.pos.",
varCountNa = NULL,
sortAscending = TRUE,
vertLine = NULL,
col = NULL,
tit = NULL,
logScale = FALSE,
las.alph = 2,
displMaxSpec = TRUE,
silent = FALSE,
debug = FALSE,
callFrom = NULL
)
Arguments
roc |
(numeric matrix or data.frame) main input: one column with thresholds and multiple columns of assoicated count data |
threColumn |
(integer or character) to specify the column with threshold-data, in typica proteomics benchmark studies this would be 'alph' (for the statistical test threshold) |
countsCol |
(character of integer, min length=2) choice of column(s) with count-data in 'roc' to be used for display, if not |
fixedCountPat |
(character) optional pattern to help identifying counts-data: if not |
varCountNa |
(character) alternative way to select the columns from 'roc': searched using |
sortAscending |
(logical) decide if data should be sorted ascending or descending |
vertLine |
(numeric) for optional vertical line, typically used to highlight alpha 0.05 |
col |
(character) custom colors, see also |
tit |
(character) cutom title |
logScale |
(logical) display threshld values (x-axis) on log-scale |
las.alph |
(numeric) orientation of label of alpha-cutoff, see also |
displMaxSpec |
(logical) display on right side of figure max count value of contributing group species |
silent |
(logical) suppress messages |
debug |
(logical) additonal messages for debugging |
callFrom |
(character) allows easier tracking of messages produced |
Details
Investigate count data prepared for plotting ROC curves : cumulative counts plot by species (along different statistical test thresholds). Note : Package wrProteo may be used to prepare input (matrix of ROC data).
Value
plot only
See Also
ecdf
, for preparing input to ROC: function summarizeForROC
in package wrProteo
Examples
set.seed(2019); test1 <- cbind(a=sample.int(n=7,size=50,repl=TRUE),
b=sample.int(n=11,size=50,repl=TRUE),c=sample.int(n=18,size=50,repl=TRUE))
test1 <- cbind(alph=seq(0,1,length.out=50),a=cumsum(test1[,1]),b=cumsum(test1[,2]),
c=cumsum(test1[,3]))
staggerdCountsPlot(test1,countsCol=c("a","b","c"))
## example below requires the package wrProteo