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Up: Component summary
Component
SegmentPlotPlots segmented chromosomal data. Any chromosomal regions defined with chromosome, start and end locations can be visualized, but the main purpose of this component is to visualize Array CGH segmentation results.
The input table must contain the following columns: Sample, chromosome, starting basepair, ending basepair. Segment call and score are optional columns. These are used to distinguish between duplications and deletions and to assign confidences or ranks to the calls, respectively.
| Version | 1.5 |
|---|---|
| Bundle | microarray |
| Categories | Latex Copy Number Analysis |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI), Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; limma (R-bioconductor) |
| Source files | component.xml SegmentPlot.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| chrSegments | CSV | Mandatory | Chromosomal segments, usually obtained from an Array CGH experiment after segmentation. |
Outputs| Name | Type | Description |
|---|---|---|
| plot | Latex | Chromosomal segments, with the significant regions highlighted if there are any. |
| SignRegion | DNARegion | The regions that are above the given threshold parameter value. The output includes a column for the frequency of the result segments. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| bpEndColumn | string | "end" | The name of the chromosomal end location column in the input file. |
| bpStartColumn | string | "start" | The name of the chromosomal start location column in the input file. |
| callColumn | string | "call" | The name of the call column in the input file. All calls are considered to be 1 if this parameter value is empty. |
| chrColumn | string | "chr" | The name of the chromosomal number column in the input file. |
| drawSampleIDs | boolean | false | Plot sample ids to the start of each row. |
| excludeChr | string | "23,24,X,Y,M" | Chromosomes that are not used in the analysis. Defaults to excluding mitochondrial and sex chromosomes. |
| gainsOrLosses | int | 0 | Determine whether to plot gains alone (1) or losses alone (-1) or both (default). |
| lineWidth | float | 3 | Line width in output plot |
| sThold | float | 0.1 | The significance threshold. Please note that this is just the fraction of samples we want the segment to be present in. |
| sampleColumn | string | "Sample" | The name of the sample name column in the input file. |
| scoreColumn | string | "" | The name of the score column in the input file. You may leave this parameter empty if the data do not contain such information. |
| scoreMerge | string | "max" | Defines an R function that is used to summarize the score values of all input calls that are contributing to an output regions. |
Test cases| Test case | Parameters▼ | IN chrSegments |
OUT plot |
OUT SignRegion |
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|---|---|---|---|---|---|---|
| case1 | (missing) | chrSegments | plot | SignRegion | ||
| case2 | properties | chrSegments | plot | SignRegion | ||
|
gainsOrLosses=1, |
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| case3 | properties | chrSegments | plot | SignRegion | ||
|
gainsOrLosses=-1, |
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| case4_InvalidCols | properties | chrSegments | (expecting failure) | (expecting failure) | ||
|
bpEndColumn=endCol, |
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| case5 | properties | chrSegments | plot | SignRegion | ||
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bpEndColumn=endCol, |
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| case6 | properties | chrSegments | plot | SignRegion | ||
|
sThold=0.1, |
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| case8 | properties | chrSegments | (missing) | SignRegion | ||
|
sThold=0.6, |
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