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mmkim1210 committed Jun 15, 2024
1 parent d595fc7 commit fd48514
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10 changes: 6 additions & 4 deletions src/plotld.jl
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Heatmap of symmetric correlation matrix `LD` with the diagonal elements on the x-axis.
# Keyword arguments
- `threshold` : threshold below which values are ignored (default to `1/9`)
- `colormap` : colormap of values (default to `cgrad(:Blues_9, 9, categorical = true)`)
- `colorrange` : start and end points of `colormap` (default to `(0, 1)`)
- `strokewidth` : width of outline around heatmap boxes (default to `0`)
```
threshold threshold below which values are ignored; default 1/9
colormap colormap of values; default cgrad(:Blues_9, 9, categorical = true)
colorrange start and end points of colormap; default (0, 1)
strokewidth width of outline around heatmap boxes; default 0
```
"""
@recipe(PlotLD, LD) do scene
Attributes(
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11 changes: 6 additions & 5 deletions src/plotlocus.jl
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Expand Up @@ -68,11 +68,12 @@ and `range2`.
Alternatively, plot within a given `chromosome` and a certain `window` around a
genomic coordinate `bp` or plot within a certain `window` around `gene`.
# Arguments
- `ld::Union{Nothing, SnpData, Tuple{SnpData, Union{AbstractString, Tuple{AbstractString, Int}}}} = nothing`:
the reference panel for which LD is calculated.
- `ymax::Real`: the maximum value for y axis.
- `window::Real = 1e6`: the window around `bp` or `gene`.
# Keyword arguments
```
ld::Union{Nothing, SnpData, Tuple{SnpData, Union{AbstractString, Tuple{AbstractString, Int}}}} default nothing
ymax maximum value for y-axis
window window around genomic coordinate or gene; default 1e6
```
"""
function plotlocus!(
ax::Axis,
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2 changes: 1 addition & 1 deletion src/plotqq.jl
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Expand Up @@ -7,7 +7,7 @@ Plot QQ plot of `P` values where the expected distribution is the uniform distri
# Keyword arguments
```
xstep x-axis ticks step size; default 1
ystep y-axis ticks step size: default 2
ystep y-axis ticks step size; default 2
```
"""
function plotqq!(
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