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PairWiseClusterPlot

Produces 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.

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