| MIAMIPLOT |
--colInChr |
|
Column name of the input chromosome. |
| MIAMIPLOT |
--colInPos |
|
Column name of the input position column. |
| MIAMIPLOT |
--colMIAMIPlotUp |
|
P-Value column that will be plotted upwards on the y-Axis. Required. |
| MIAMIPLOT |
--colMIAMIPlotDown |
|
P-Value column that will be plotted downwards on the y-Axis. Required. |
| MIAMIPLOT |
--astrDefaultColourChr |
"c(""gray51"",""gray66"")" |
"Array of length two. Defines the changing chromosome colours. Optional. Default: gray51;gray67 |
| MIAMIPLOT |
--arcdColourCrit |
|
array of R code expressions with criteria for varying colours |
| MIAMIPLOT |
--astrColour |
|
array of colours according to criteria |
| MIAMIPLOT |
--numDefaultSymbol |
19 |
defulat symbol |
| MIAMIPLOT |
--numDefaultCex |
0.4 |
default cex |
| MIAMIPLOT |
--arcdSymbolCrit |
|
array of R code expressions with criteria for varying symbols |
| MIAMIPLOT |
--anumSymbol |
-1 |
array of symbol values (R's pch parameter) |
| MIAMIPLOT |
--arcdCexCrit |
|
array of cex values according to criteria |
| MIAMIPLOT |
--anumCex |
-1 |
array of symbol sizes (R's cex parameter) |
| MIAMIPLOT |
--fileAnnot |
|
annotation file |
| MIAMIPLOT |
--numAnnotPosLim |
500000 |
|
| MIAMIPLOT |
--numAnnotPvalLim |
1 |
|
| MIAMIPLOT |
--fileAnnotUp |
|
|
| MIAMIPLOT |
--numAnnotUpPosLim |
-1 |
|
| MIAMIPLOT |
--numAnnotUpPvalLim |
-1 |
|
| MIAMIPLOT |
--fileAnnotDown |
|
|
| MIAMIPLOT |
--numAnnotDownPosLim |
-1 |
|
| MIAMIPLOT |
--numAnnotDownPvalLim |
-1 |
|
| MIAMIPLOT |
--numPvalOffset |
1 |
|
| MIAMIPLOT |
--arcdAdd2Plot |
|
array of R code expressions that will be added to the plot (eg text(…)) |
| MIAMIPLOT |
--anumAddPvalLine |
5.00E-08 |
numeric value where horizontal P Value line will be added |
| MIAMIPLOT |
--astrAddPvalLineCol |
red |
|
| MIAMIPLOT |
--anumAddPvalLineLty |
6 |
type of horizontal line (R's lty parameter) |
| MIAMIPLOT |
--blnYAxisBreak |
FALSE |
logical whether y axis should be broken at certain value |
| MIAMIPLOT |
--numYAxisBreak |
22 |
|
| MIAMIPLOT |
--strPlotName |
miami |
plot name (added to file name to indicate this plot) |
| MIAMIPLOT |
--strFormat |
png |
graphic file format |
| MIAMIPLOT |
--numCexAxis |
1.5 |
cex for axis |
| MIAMIPLOT |
--numCexLab |
2 |
cex for lables |
| MIAMIPLOT |
--numWidth |
1600, |
Width of the plot in pixel. |
| MIAMIPLOT |
--numHeight |
1200, |
Height of the plot in pixel. |
| MIAMIPLOT |
--anumParMar |
c(7,6,4,10) |
array of four 'par' parameters |
| MIAMIPLOT |
--anumParMgp |
c(3,1,0) |
array of three 'mgp' parameters |
| MIAMIPLOT |
--strParBty |
o |
plot param 'bty' |
| MIAMIPLOT |
--blnLogPval |
FALSE |
is P value logarithmized? |
| MIAMIPLOT |
--astrDefaultColourChrUp |
|
"Array of length two. Defines the changing upward chromosome colours. Optional. Default: gray51;gray69 |
| MIAMIPLOT |
--arcdColourCritUp |
|
array of R code expressions with criteria for varying colours upward |
| MIAMIPLOT |
--astrColourUp |
|
array of colours according to criteria upward |
| MIAMIPLOT |
--numDefaultSymbolUp |
-1 |
defulat symbol upward |
| MIAMIPLOT |
--numDefaultCexUp |
-1 |
default cex upward |
| MIAMIPLOT |
--arcdSymbolCritUp |
|
array of R code expressions with criteria for varying symbols upward |
| MIAMIPLOT |
--anumSymbolUp |
-1 |
array of symbol values for upward plot (R's pch parameter) |
| MIAMIPLOT |
--arcdCexCritUp |
|
array of cex values according to criteria |
| MIAMIPLOT |
--anumCexUp |
-1 |
array of symbol sizes upward plot (R's cex parameter) |
| MIAMIPLOT |
--astrDefaultColourChrDown |
|
"Array of length two. Defines the changing downward chromosome colours. Optional. Default: gray51;gray68 |
| MIAMIPLOT |
--arcdColourCritDown |
|
array of R code expressions with criteria for varying colours downward |
| MIAMIPLOT |
--astrColourDown |
|
array of colours according to criteria downward |
| MIAMIPLOT |
--numDefaultSymbolDown |
-1 |
defulat symbol downward |
| MIAMIPLOT |
--numDefaultCexDown |
-1 |
default cex downward |
| MIAMIPLOT |
--arcdSymbolCritDown |
|
array of R code expressions with criteria for varying symbols downward |
| MIAMIPLOT |
--anumSymbolDown |
-1 |
array of symbol values for downward plot (R's pch parameter) |
| MIAMIPLOT |
--arcdCexCritDown |
|
array of cex values according to criteria |
| MIAMIPLOT |
--anumCexDown |
-1 |
array of symbol sizes downward plot (R's cex parameter) |
| MIAMIPLOT |
--blnPlotVerticalLines |
TRUE |
logical whether vertical lines at chrom breaks should be added |
| MIAMIPLOT |
--numYAxisLim |
Inf |
|