Manhattan Plots : General parameters in scatter plots
# armLengths
Manhattan Chromosomes arm length is a sorted array by chromosome with the length in base pairs for each chromosomeshort arm. It has to have the same dimesions as the chromosomeLengths
Type:
array
Default:
[]
Used in:
Scatter2D
# chromosomeLengths
Manhattan Chromosomes length is a sorted array by chromosome with the length in base pairs for each chromosome. It is required when scatterType is manhattan
Type:
array
Default:
[]
Used in:
Scatter2D
# manhattanCNV
Sample name included in the data.y.smps object used to map to the copy number value
Type:
string
Default:
Used in:
Scatter2D
# manhattanColors
Colors for the manhattan plots alternative chromosomes
Type:
array
Default:
[rgb(128,128,128), rgb(135,206,235)]
Used in:
Scatter2D
# manhattanContrastColor
# manhattanMarkerChromosomeNumber
Sample name included in the data.y.smps object used to map to the chromosome number
Type:
string
Default:
Used in:
Scatter2D
# manhattanMarkerLogPValue
Sample name included in the data.y.smps object used to map to the negative log 10 p value
Type:
string
Default:
Used in:
Scatter2D
# manhattanMarkerPosition
Sample name included in the data.y.smps object used to map to the position in base pairs
Type:
string
Default:
Used in:
Scatter2D
# manhattanRangeEnd
Sample name included in the data.y.smps object used to map the end position
Type:
string
Default:
Used in:
Scatter2D
# manhattanRangeLineWidth
# manhattanRangeStart
Sample name included in the data.y.smps object used to map the start position
Type:
string
Default:
Used in:
Scatter2D
# showmanhattanRangeMiddle
Flag to show/hide the show dot in the middle of the range in manhattan plots
Type:
boolean
Default:
false
Used in:
Scatter2D
