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Up: Component summary
Component
PairWiseClusterPlotProduces pairwise scatter plots from clustered and filtered data. The points not present in filtered data will be plotted in grey colour.
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Ali Oghabian (ali.oghabian@helsinki.fi), Erkka Valo (erkka.valo@helsinki.fi) |
| Requires | R |
| Source files | component.xml PairWiseClusterPlot.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| clusterFiles | CSVList | Optional | CSV files with clusterd rows to plot. |
| clusters | Array<CSV> | Optional | CSV files with clusterd rows to plot. |
| filteredFiles | CSVList | Optional | Filtered CSV files with clusterd rows. The elements in the array
should have the same keys as in the clusteredFiles input.
A element should contain a subset of rows of the corresponding
element in clusteredFiles. The rows not present in
the filtered data will be plotted in grey. |
| filtered | Array<CSV> | Optional | Filtered CSV files with clusterd rows. The elements in the array
should have the same keys as in the clusters input.
A element should contain a subset of rows of the corresponding
element in clusters. The rows not present in the filtered
data will be plotted in grey. |
Outputs| Name | Type | Description |
|---|---|---|
| report | Latex | The pairwise scatter plots in a LaTeX document. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| caption | string | "Cluster plot for input file %s" | LaTeX caption of each figure. The caption may contain one %s placeholder, which is replaced with the input file name. |
| channelsToPlot | string | (no default) | The names of the columns to be plotted as a comma-separated list. |
| clusterClustIDCol | string | "cluster" | The name of the column in the clusterFiles/clusters which contains the cluster IDs to which the rows are assigned. |
| clusterIDCol | string | "Event" | The name of the column in the clusterFiles/clusters which represents the IDs of the rows. |
| filteredIDCol | string | "Event" | The name of the column in the filteredFiles/filtered which represents the IDs of the rows. |
| pagebreak | boolean | false | Should the result document start with a page break. |
| pch | string | "." | The type and shape of plotting points. Numbers (e.g. "2") and characters (e.g. ".") are possible. |
| plotClusterCentres | boolean | false | If true, the centres of the clusters are plotted. The center is defined in every dimension using the mean value for the cluster. |
| plotType | string | "regular2d" | The type of the plot. The choices are regular2d, and regular3d. |
| presentationType | string | "points" | The plot types similar to "pch" parameter in R plottings. "points" or "p", "lines" or "l", "pointsLines" or "b", "histogram" or "h", "stairs" or "s", "otherStairs" or "S" (as in R), "overplotted" or "o", and "linesApart" or "c" (as in R) are the options. |
| sectionTitle | string | "" | Title for a new latex section. If non is given, a new section is not created. |
| sectionType | string | "section" | Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty. |