update

src/plot_logo.jl

@@ -36,24 +36,6 @@ end
 
 
 
-@userplot ArrowPlot
-@recipe function f(data::ArrowPlot)
-    coords = data.args[1]
-    color --> :grey
-    for coord in coords
-        for v in coord
-            @series begin
-                fill := 0
-                lw --> 0
-                # label --> k
-                v.x, v.y
-            end
-        end
-    end
-end
-
-
-
 @userplot LogoPlot
 @recipe function f(data::LogoPlot; 
                    rna=false, 

src/plot_logo_w_arr_gaps.jl

@@ -0,0 +1,59 @@
+
+@userplot ArrowPlot
+@recipe function f(data::ArrowPlot)
+    coords = data.args[1]
+    color --> :grey
+    for coord in coords
+        for v in coord
+            @series begin
+                fill := 0
+                lw --> 0
+                # label --> k
+                v.x, v.y
+            end
+        end
+    end
+end
+
+"""
+ds_mat: Matrix of distances between the pfms
+    e.g. 12 6
+         32 8
+    number of rows = number of "modes" of distances
+    number of columns = number of distance in between the pfms
+weights: weights for each mode of distances
+optional parameters:
+    given_num_cols: the total number of columns that will be occupied for all the arrow-shapes
+    arrow_shape_scale_ratio: the ratio by which the width of the arrow-shapes will be scaled
+    height_top: the maximum height of the arrow-shapes
+"""
+function logoplot_with_arrow_gaps(pfms, 
+    ds_mats::Matrix{T},
+    weights::Vector{T};
+    given_num_cols::Int=15,
+    arrow_shape_scale_ratio::Real=0.7,
+    height_top::Real=1.7
+    ) where T<:Real
+
+    @assert length(pfms)-1 == size(ds_mats, 2) "The number of columns in ds_mats should be equal to the length of pfms - 1"
+    @assert length(weights) == size(ds_mats, 1) "The number of rows in ds_mats should be equal to the length of weights"
+
+    coords_mat, pfm_starts, total_pfm_cols, total_d_cols = 
+        make_arrow_shapes(ds_mats, weights, given_num_cols, pfms;
+        arrow_shape_scale_ratio=arrow_shape_scale_ratio, height_top=height_top)
+
+    p = nothinglogo(total_pfm_cols + total_d_cols);    
+
+    for (ind, pfm) in enumerate(pfms)
+        logo_x_offset = pfm_starts[ind]
+        logoplot!(p, pfm, PlotPWM.bg; 
+                    dpi=65,
+                    setup_off=true, 
+                    logo_x_offset=logo_x_offset)
+    end
+
+    for col in eachcol(coords_mat)
+        arrowplot!(p, col)
+    end
+    return p
+end

tmp3.jl

@@ -227,6 +227,50 @@ inds_sorted = sortperm(weights)
 weights = weights[inds_sorted]
 ds_mats = @view ds_mats[inds_sorted, :]
 
+"""
+ds_mat: Matrix of distances between the pfms
+    e.g. 12 6
+         32 8
+    number of rows = number of "modes" of distances
+    number of columns = number of distance in between the pfms
+weights: weights for each mode of distances
+optional parameters:
+    given_num_cols: the total number of columns that will be occupied for all the arrow-shapes
+    arrow_shape_scale_ratio: the ratio by which the width of the arrow-shapes will be scaled
+    height_top: the maximum height of the arrow-shapes
+"""
+function logoplot_with_arrow_gaps(pfms, 
+    ds_mats::Matrix{T},
+    weights::Vector{T};
+    given_num_cols::Int=15,
+    arrow_shape_scale_ratio::Real=0.7,
+    height_top::Real=1.7
+    ) where T<:Real
+
+    @assert length(pfms)-1 == size(ds_mats, 2) "The number of columns in ds_mats should be equal to the length of pfms - 1"
+    @assert length(weights) == size(ds_mats, 1) "The number of rows in ds_mats should be equal to the length of weights"
+
+    coords_mat, pfm_starts, total_pfm_cols, total_d_cols = 
+        make_arrow_shapes(ds_mats, weights, given_num_cols, pfms;
+        arrow_shape_scale_ratio=arrow_shape_scale_ratio, height_top=height_top)
+
+    p = nothinglogo(total_pfm_cols + total_d_cols);    
+
+    for (ind, pfm) in enumerate(pfms)
+        logo_x_offset = pfm_starts[ind]
+        logoplot!(p, pfm, PlotPWM.bg; 
+                    dpi=65,
+                    setup_off=true, 
+                    logo_x_offset=logo_x_offset)
+    end
+
+    for col in eachcol(coords_mat)
+        arrowplot!(p, col)
+    end
+    return p
+end
+
+
 coords_mat, pfm_starts, total_pfm_cols, total_d_cols = 
     make_arrow_shapes(ds_mats, weights, 15, pfms;
     arrow_shape_scale_ratio=0.7, height_top=1.7)