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SpatialPlot

Creates 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

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