Up: Component summary
Up: Component summary
Component
GatingSummaryGenerate summay report table and heatmap.
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Ping Chen (ping.chen@helsinki.fi) |
| Requires | R ; fields (R-package) |
| Source files | component.xml GatingSummary.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| summaries | CSVList | Mandatory | A directory with CSV files which contain summarised intensities for each cluster. |
| sampleAnnotation | CSV | Mandatory | A CSV annotation file with columns 'File', 'Stimulus', 'Panel' and 'PatientID'. |
| panel | CSV | Mandatory | A CSV file with columns 'Panel' and 'Antibody' contains antibodies measured in each panel. Antibodies measured in each pannel are comma-separated. |
| population | CSVList | Mandatory | Automatically gated cell populations. |
Outputs| Name | Type | Description |
|---|---|---|
| summaryResult | CSVList | Summary tables for each patient. |
| report | Latex | Visualization of summarised results. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| NAcolor | string | "pink" | Color to use for missing value (NA). |
| colorSchema | string | "greenred" | The color schema for plotting. It can be one of 'greenred', 'redgreen', 'redblue', 'bluered', 'heatcolor', 'rainbow' or 'blackyellowwhite'. |
| pagebreak | boolean | true | Tells if the result document should start with a page break. |
| rotate | boolean | false | Rotate output table if there are too many columns. |
| scale | float | 0.6 | A scaling factor for the figure. |
| targetPop | string | "Monocytes" | A string specifies the target population name measured for each patient. |
| type | string | "median" | A string specifies how to merge data in multiple populations. It can be 'median' or 'mean'. |
| width | float | 2 | Width (inches) of each square in heatmap. |
Test cases| Test case | Parameters▼ | IN summaries |
IN sampleAnnotation |
IN panel |
IN population |
OUT summaryResult |
OUT report |
|---|---|---|---|---|---|---|---|
| case1 | properties | summaries | sampleAnnotation | panel | population | summaryResult | report |
|
colorSchema=greenred |
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| case2 | (missing) | summaries | sampleAnnotation | panel | population | summaryResult | report |
| case3 | properties | summaries | sampleAnnotation | panel | population | summaryResult | report |
|
colorSchema=greenred, |
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