Up: Component summary
Up: Component summary
Component
SpatialPlotCreates spatial plots for red/green channels, log ratios and spot quality.
| Version | 1.4 |
|---|---|
| Bundle | microarray |
| Categories | Latex Quality Control Plot |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml SpatialPlot.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| geneAnnotation | AnnotationTable | Mandatory | Must contain columns Row, Column. |
| channel1 | LogMatrix | Mandatory | Channel expression data 1. |
| channel2 | LogMatrix | Optional | Channel expression data 2. |
| logratio | LogMatrix | Optional | Log ratio data. If present, two kinds of plots are created: spatial plots for the actual expression values and quality plots that show locations of filtered (NA) spots. |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | Latex subsection containing the spatial plot. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| channelTitle1 | string | "Green channel" | Main title of channel plot 1. Sample name is appended to this string, so the final title would be, for example, "Green channel (SAMPLE NAME)". |
| channelTitle2 | string | "Red channel" | Main title of channel plot 2. Sample name is appended to this string, so the final title would be, for example, "Red channel (SAMPLE NAME)". |
| height | float | 11 | Height of each plot in cm. |
| highQuantile | float | 0.95 | Quantile that determines the contrast of the images in the high intensity end. All values above highQuantile get the color for the highest value. |
| logratioTitle | string | "Log ratio" | Main title of the log ratio plot. Sample name is appended to this string, so the final title would be, for example, "Log Ratio (SAMPLE NAME)". |
| lowQuantile | float | 0.05 | Quantile that determines the contrast of the images in the low intensity end. All values below lowQuantile get the color for the lowest value. |
| width | float | 14 | Width of each plot in cm. |
Test cases| Test case | Parameters▼ | IN geneAnnotation |
IN channel1 |
IN channel2 |
IN logratio |
OUT report |
|---|---|---|---|---|---|---|
| case1 | (missing) | geneAnnotation | channel1 | channel2 | logratio | report |