Description Usage Arguments Details Value
Visit each node in an object of class XMLNode and gather information to print one line for each vertex which represents the location of a cell on the slide [NOTE: DOUBLE CHECK THIS FOR ACCURACY]
1 2 3 | parseAnnotationXML(node, fovName = NULL, outFile = NULL, LineColor = "",
Name = "", Visible = "", RegionType = "", HasEndcaps = 0,
NegativeROA = 0, boundaryColors = NULL)
|
node |
object of class XMLNode containing Halo annotations for one FOV |
fovName |
unique identifier of FOV |
outFile |
output file |
LineColor |
code for line color of the annotation ["655280"|"65535"|"255"] |
Name |
name of the annotation |
Visible |
logical indicating whether annotation is visible [????] |
RegionType |
region type *Note: any region with type other than Polygon is skipped |
HasEndcaps |
[???] |
NegativeROA |
[???] |
boundaryColors |
a list including hex colors for Tum, Exc, and Epi boundaries; default=list("65280"="Tum", "65535"="Exc", "255"="Epi") |
Output is a tab-delimited file containing: 1) FOV name 2) Annotation number 3) Line color 4) Name 5) Visible 6) Region number 7) Region type 8) HasEndcaps 9) NegativeROA 10) X coordinate 11) Y coordinate ***(negative of what is output by Halo)*** 12) Region according to color (Tumor, Exclusion, Epidermis)
nothing
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