| MHPLOT |
--colMHPlot |
|
P-Value column that will be plotted on the y-Axis. Required. |
| MHPLOT |
--colInChr |
|
Column name of the input chromosome. |
| MHPLOT |
--colInPos |
|
Column name of the input position column. |
| MHPLOT |
--astrDefaultColourChr |
"c(""gray51"",""gray66"")" |
"Array of length two. Defines the changing chromosome colours. Optional. Default: gray51;gray66 |
| MHPLOT |
--arcdColourCrit |
|
array of R code expressions with criteria for varying colours |
| MHPLOT |
--astrColour |
|
array of colours according to criteria |
| MHPLOT |
--numPvalOffset |
1 |
pvalue offset to speed up plot |
| MHPLOT |
--arcdAdd2Plot |
|
array of R code expressions that will be added to the plot (eg text(…)) |
| MHPLOT |
--anumAddPvalLine |
5.00E-08 |
numeric value where horizontal P Value line will be added |
| MHPLOT |
--astrAddPvalLineCol |
red |
colour of added line |
| MHPLOT |
--anumAddPvalLineLty |
6 |
type of horizontal line (R's lty parameter) |
| MHPLOT |
--blnYAxisBreak |
FALSE |
logical whether y axis should be broken at certain value |
| MHPLOT |
--numYAxisBreak |
22 |
value to break y axis |
| MHPLOT |
--strPlotName |
mh |
plot name (added to file name to indicate this plot) |
| MHPLOT |
--strFormat |
png |
graphic file format |
| MHPLOT |
--numCexAxis |
1.5 |
cex for axis |
| MHPLOT |
--numCexLab |
2 |
cex for lables |
| MHPLOT |
--numWidth |
1600, |
Width of the plot in pixel. |
| MHPLOT |
--numHeight |
600, |
Height of the plot in pixel. |
| MHPLOT |
--anumParMar |
c(7,6,4,10) |
array of four 'par' parameters |
| MHPLOT |
--anumParMgp |
c(3,1,0) |
array of three 'mgp' parameters |
| MHPLOT |
--strParBty |
o |
plot param 'bty' |
| MHPLOT |
--blnLogPval |
FALSE |
is P value logarithmized? |
| MHPLOT |
--numDefaultSymbol |
19 |
defulat symbol |
| MHPLOT |
--numDefaultCex |
0.4 |
default cex |
| MHPLOT |
--arcdSymbolCrit |
|
array of R code expressions with criteria for varying symbols |
| MHPLOT |
--anumSymbol |
-1 |
array of symbol values accorind to criteria (R's pch parameter) |
| MHPLOT |
--arcdCexCrit |
|
array of R code expressions with criteria for varying cex sizes |
| MHPLOT |
--anumCex |
-1 |
array of cex values accorind to criteria (R's cex parameter) |
| MHPLOT |
--fileAnnot |
|
annotation file |
| MHPLOT |
--numAnnotPosLim |
500000 |
|
| MHPLOT |
--numAnnotPvalLim |
1 |
|
| MHPLOT |
--strColourNovel |
|
|
| MHPLOT |
--rcdAnnotSignif |
|
|
| MHPLOT |
--blnPlotVerticalLines |
TRUE |
logical whether vertical lines at chrom breaks should be added |
| MHPLOT |
--numYAxisLim |
Inf |
y axis limit |