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Fixed scales on plots Topography, Surface and axis on spectrum

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This commit is contained in:
Pixelguy14 2025-02-20 15:22:54 -06:00
parent 0456abb70b
commit 3714b404cd
2 changed files with 31 additions and 8 deletions
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6
app.jl
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@ -168,11 +168,13 @@ include("./julia_imzML_visual.jl")
title="Spectrum plot", title="Spectrum plot",
xaxis=PlotlyBase.attr( xaxis=PlotlyBase.attr(
title="<i>m/z</i>", title="<i>m/z</i>",
showgrid=true showgrid=true,
tickformat = ".3g"
), ),
yaxis=PlotlyBase.attr( yaxis=PlotlyBase.attr(
title="Intensity", title="Intensity",
showgrid=true showgrid=true,
tickformat = ".3g"
), ),
margin=attr(l=0,r=0,t=120,b=0,pad=0) margin=attr(l=0,r=0,t=120,b=0,pad=0)
) )

33
julia_imzML_visual.jl
View File

@ -252,6 +252,12 @@ function loadContourPlot(interfaceImg::String)
y=1:size(elevation_smoothed, 1) y=1:size(elevation_smoothed, 1)
X=repeat(reshape(x, 1, length(x)), length(y), 1) X=repeat(reshape(x, 1, length(x)), length(y), 1)
Y=repeat(reshape(y, length(y), 1), 1, length(x)) Y=repeat(reshape(y, length(y), 1), 1, length(x))
# Define tick values and text for colorbars
min_val = minimum(elevation_smoothed)
max_val = maximum(elevation_smoothed)
tickV = range(min_val, stop=max_val, length=8)
tickT = log_tick_formatter(collect(tickV))
layout=PlotlyBase.Layout( layout=PlotlyBase.Layout(
title="2D topographic map of $cleaned_img", title="2D topographic map of $cleaned_img",
@ -270,8 +276,10 @@ function loadContourPlot(interfaceImg::String)
y=-Y[:, 1], # Use the first column y=-Y[:, 1], # Use the first column
contours_coloring="Viridis", contours_coloring="Viridis",
colorscale="Viridis", colorscale="Viridis",
colorbar=attr( colorbar = attr(
tickformat=".2g" tickvals = tickV,
ticktext = tickT,
tickmode = "array"
) )
) )
plotdata=[trace] plotdata=[trace]
@ -291,15 +299,24 @@ function loadSurfacePlot(interfaceImg::String)
img_gray=Gray.(img) # Convert to grayscale img_gray=Gray.(img) # Convert to grayscale
img_array=Array(img_gray) img_array=Array(img_gray)
elevation=Float32.(Array(img_array)) ./ 255.0 # Normalize between 0 and 1 elevation=Float32.(Array(img_array)) ./ 255.0 # Normalize between 0 and 1
# Smooth the image # Smooth the image
sigma=3.0 sigma=3.0
kernel=Kernel.gaussian(sigma) kernel=Kernel.gaussian(sigma)
elevation_smoothed=imfilter(elevation, kernel) elevation_smoothed=imfilter(elevation, kernel)
# Create the X, Y meshgrid coordinates # Create the X, Y meshgrid coordinates
x=1:size(elevation_smoothed, 2) x=1:size(elevation_smoothed, 2)
y=1:size(elevation_smoothed, 1) y=1:size(elevation_smoothed, 1)
X=repeat(reshape(x, 1, length(x)), length(y), 1) X=repeat(reshape(x, 1, length(x)), length(y), 1)
Y=repeat(reshape(y, length(y), 1), 1, length(x)) Y=repeat(reshape(y, length(y), 1), 1, length(x))
# Define tick values and text for colorbars
min_val = minimum(elevation_smoothed)
max_val = maximum(elevation_smoothed)
tickV = range(min_val, stop=max_val, length=8)
tickT = log_tick_formatter(collect(tickV))
# Calculate the number of ticks and aspect ratio for the 3d plot # Calculate the number of ticks and aspect ratio for the 3d plot
x_nticks=min(20, length(x)) x_nticks=min(20, length(x))
y_nticks=min(20, length(y)) y_nticks=min(20, length(y))
@ -336,8 +353,10 @@ function loadSurfacePlot(interfaceImg::String)
project_z=true project_z=true
), ),
colorscale="Viridis", colorscale="Viridis",
colorbar=attr( colorbar = attr(
tickformat=".2g" tickvals = tickV,
ticktext = tickT,
nticks=8
) )
) )
plotdata=[trace3D] plotdata=[trace3D]
@ -418,11 +437,13 @@ function sumSpectrumPlot(mzmlRoute::String)
title="SUM spectrum plot", title="SUM spectrum plot",
xaxis=PlotlyBase.attr( xaxis=PlotlyBase.attr(
title="<i>m/z</i>", title="<i>m/z</i>",
showgrid=true showgrid=true,
tickformat = ".3g"
), ),
yaxis=PlotlyBase.attr( yaxis=PlotlyBase.attr(
title="Intensity", title="Intensity",
showgrid=true showgrid=true,
tickformat = ".3g"
), ),
autosize=false, autosize=false,
margin=attr(l=0,r=0,t=120,b=0,pad=0) margin=attr(l=0,r=0,t=120,b=0,pad=0)