design matrix

unfoldtoolbox · Nov 15, 2023 · bf6324e · bf6324e
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diff --git a/docs/src/tutorials/designmatrix.md b/docs/src/tutorials/designmatrix.md
@@ -1,6 +1,6 @@
 # [Designmatrix Visualization](@id dm_vis)
 
-Here we discuss designmatrix visualization. 
+Here we discuss design matrix visualization. 
 Make sure you have looked into the [installation instructions](@ref install_instruct) section. 
 
 ## Include used Modules
@@ -31,20 +31,18 @@ plot_designmatrix(designmatrix(uf))
 # kwargs `plot_designmatrix(...; ...)`.
 
 
-- sortData (boolean,false)  - Indicating whether the data is sorted; using sortslices() of Base Julia. 
+- `sort_data` (bool, `true`): indicates whether the data is sorted; using sortslices() of Base Julia. 
 
-
-In order to make the designmatrix easier to read, you may want to sort it.
+To make the design matrix easier to read, you may want to sort it.
 ```
 plot_designmatrix(designmatrix(uf); sortData=true)
 ```
 
-- standardizeData (boolean, false) - Indicating whether the data is standardized, mapping the values between 0 and 1. 
-- xTicks (number, nothing)
-
-Indicating the number of labels on the x-axis. Behavior if specified in configuration:
-    - xTicks = 0: no labels are placed.
-    - xTicks = 1: first possible label is placed.
-    - xTicks = 2: first and last possible labels are placed.
-    - 2 < xTicks < number of labels: xTicks-2 labels are placed between the first and last.
-    - xTicks ≥ number of labels: all labels are placed.
+- `standardize_data` (bool,`true`): indicates whether the data is standardized by pointwise division of the data with its sampled standard deviation.
+- `sort_data` (bool, `true`): indicates whether the data is sorted; using sortslices() of Base Julia. 
+- `xticks` (`nothing`): returns the number of labels on the x-axis. Behavior is set in the configuration:
+    - xticks = 0: no labels are placed.
+    - xticks = 1: first possible label is placed.
+    - xticks = 2: first and last possible labels are placed.
+    - 2 < xticks < `number of labels`: equally distribute the labels.
+    - xticks ≥ `number of labels`: all labels are placed.
diff --git a/src/plot_designmatrix.jl b/src/plot_designmatrix.jl
@@ -1,73 +1,70 @@
 """ 
-    plot_designmatrix!(f::Union{GridPosition, GridLayout, Figure}, plotData::Unfold.DesignMatrix; kwargs...)
-    plot_designmatrix(plotData::Unfold.DesignMatrix; kwargs...)
+    plot_designmatrix!(f::Union{GridPosition, GridLayout, Figure}, data::Unfold.DesignMatrix; kwargs...)
+    plot_designmatrix(data::Unfold.DesignMatrix; kwargs...)
         
 
 Plot a designmatrix. 
 ## Arguments:
-- `f::Union{GridPosition, GridLayout, Figure}`: Figure or GridPosition (e.g. f[2, 3]) that the plot should be drawn into. New axis is created.
-- `plotData::Unfold.DesignMatrix`: Data for the plot visualization.
+- `f::Union{GridPosition, GridLayout, Figure}`: Figure or GridPosition (e.g. f[2, 3]) in which the plot will be placed into. A new axis is created.
+- `data::Unfold.DesignMatrix`: data for the plot visualization.
 
 ## kwargs
-- `standardizeData`: (bool,`true`) - Indicating whether the data is standardized by pointwise division of the data with its sampled standard deviation.
-- `sortData`: (bool, `true`) - Indicating whether the data is sorted; using sortslices() of Base Julia. 
-- `xTicks`: (`nothing`) 
-
-Indicating the number of labels on the x-axis.
-Behavior if specified in configuration:
-- xTicks = 0: no labels are placed.
-- xTicks = 1: first possible label is placed.
-- xTicks = 2: first and last possible labels are placed.
-- 2 < xTicks < `number of labels`: Equally distribute the labels.
-- xTicks ≥ `number of labels`: all labels are placed.
+- `standardize_data` (bool,`true`): indicates whether the data is standardized by pointwise division of the data with its sampled standard deviation.
+- `sort_data` (bool, `true`): indicates whether the data is sorted; using sortslices() of Base Julia. 
+- `xticks` (`nothing`): returns the number of labels on the x-axis. Behavior is set in the configuration:
+    - xticks = 0: no labels are placed.
+    - xticks = 1: first possible label is placed.
+    - xticks = 2: first and last possible labels are placed.
+    - 2 < xticks < `number of labels`: equally distribute the labels.
+    - xticks ≥ `number of labels`: all labels are placed.
 
 $(_docstring(:designmat))
 
 ## Return Value:
 A figure displaying the designmatrix. 
 """
-plot_designmatrix(plotData::Unfold.DesignMatrix; kwargs...) =
-    plot_designmatrix!(Figure(), plotData; kwargs...)
+plot_designmatrix(data::Unfold.DesignMatrix; kwargs...) =
+    plot_designmatrix!(Figure(), data; kwargs...)
 function plot_designmatrix!(
     f::Union{GridPosition,GridLayout,Figure},
-    plotData::Unfold.DesignMatrix;
-    xTicks = nothing,
-    sortData = false,
-    standardizeData = false,
+    data::Unfold.DesignMatrix;
+    xticks = nothing,
+    sort_data = false,
+    standardize_data = false,
     kwargs...,
 )
     config = PlotConfig(:designmat)
     config_kwargs!(config; kwargs...)
-    designmat = Unfold.get_Xs(plotData)
-    if standardizeData
+    designmat = Unfold.get_Xs(data)
+    if standardize_data
         designmat = designmat ./ std(designmat, dims = 1)
         designmat[isinf.(designmat)] .= 1.0
     end
 
     if isa(designmat, SparseMatrixCSC)
-        if sortData
-            @warn "Sorting does not make sense for timeexpanded designmatrices. sortData has been set to `false`"
+        if sort_data
+            @warn "Sorting does not make sense for time-expanded designmatrices. sort_data has been set to `false`"
 
-           sortData = false
+           sort_data = false
         end
         designmat = Matrix(designmat[end÷2-2000:end÷2+2000, :])
     end
 
-    if sortData
+    if sort_data
         designmat = Base.sortslices(designmat, dims = 1)
     end
-    labels = Unfold.get_coefnames(plotData)
+    labels = Unfold.get_coefnames(data)
 
     lLength = length(labels)
-    # only change xTicks if we want less then all
-    if (xTicks !== nothing && xTicks < lLength)
-        @assert(xTicks >= 0, "xTicks shouldn't be negative")
-        # sections between xTicks
-        sectionSize = (lLength - 2) / (xTicks - 1)
+    # only change xticks if we want less then all
+    if (xticks !== nothing && xticks < lLength)
+        @assert(xticks >= 0, "xticks shouldn't be negative")
+        # sections between xticks
+        sectionSize = (lLength - 2) / (xticks - 1)
         newLabels = []
 
         # first tick. Empty if 0 ticks
-        if xTicks >= 1
+        if xticks >= 1
             push!(newLabels, labels[1])
         else
             push!(newLabels, "")
@@ -76,15 +73,15 @@ function plot_designmatrix!(
         # fill in ticks in the middle
         for i = 1:(lLength-2)
             # checks if we're at the end of a section, but NO tick on the very last section
-            if i % sectionSize < 1 && i < ((xTicks - 1) * sectionSize)
+            if i % sectionSize < 1 && i < ((xticks - 1) * sectionSize)
                 push!(newLabels, labels[i+1])
             else
                 push!(newLabels, "")
             end
         end
 
         # last tick at the end
-        if xTicks >= 2
+        if xticks >= 2
             push!(newLabels, labels[lLength-1])
         else
             push!(newLabels, "")

diff --git a/test/test_dm.jl b/test/test_dm.jl
@@ -6,13 +6,13 @@ uf = example_data("UnfoldLinearModel")
 end
 
 @testset "sort data" begin
-    plot_designmatrix(designmatrix(uf); sortData = true)
+    plot_designmatrix(designmatrix(uf); sort_data = true)
 end
 
 
 @testset "designmatrix plot in GridLayout" begin
     f = Figure(resolution=(1200, 1400))
     ga = f[1, 1] = GridLayout()
-    plot_designmatrix!(ga, designmatrix(uf); sortData = true)
+    plot_designmatrix!(ga, designmatrix(uf); sort_data = true)
     f
 end