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Improved the way it handles plotting

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José Julián Sierra Álvarez 2024-09-11 15:55:00 -06:00 committed by GitHub
parent 60441a28d8
commit e7e751c143
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1 changed files with 15 additions and 11 deletions
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26
app.jl
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@ -47,8 +47,7 @@ using Statistics
@in msgimg = "" @in msgimg = ""
@in msgtriq = "" @in msgtriq = ""
@out full_route = "" @out full_route = ""
@out dims = 0 @out full_routeMz = ""
@out MicroscansMax = 0
layoutSpectra = PlotlyBase.Layout( layoutSpectra = PlotlyBase.Layout(
title = "Spectra Plot", title = "Spectra Plot",
xaxis = PlotlyBase.attr( xaxis = PlotlyBase.attr(
@ -59,8 +58,6 @@ using Statistics
title = "Intensity", title = "Intensity",
showgrid = true showgrid = true
), ),
width = 450,
height = 500
) )
traceSpectra = PlotlyBase.scatter(x=[], y=[], mode="lines+markers") traceSpectra = PlotlyBase.scatter(x=[], y=[], mode="lines+markers")
@out plotdata = [traceSpectra] @out plotdata = [traceSpectra]
@ -79,6 +76,19 @@ using Statistics
if contains(file_name,".imzML") if contains(file_name,".imzML")
warning_fr = "" warning_fr = ""
full_route = joinpath( file_route, file_name ) full_route = joinpath( file_route, file_name )
if isfile(full_route) # check if the file exists
full_routeMz = split( full_route, "." )[1] * ".mzML" # Splitting the route from imzml to mzml so the plotting can work
if isfile(full_routeMz) # check if there is an mzML file around
spectraMz = LoadMzml(full_routeMz)
# dims = size(spectraMz)
# scansMax = dims[2] # we get the total of scansMax
# traceSpectra = PlotlyBase.scatter(x = spectraMz[1, 1], y = spectraMz[2, 1], mode="lines")
traceSpectra = PlotlyBase.scatter(x = mean(spectraMz[1,:]), y = mean(spectraMz[2,:]), mode="lines")
plotdata = [traceSpectra] # we add the data of spectra to the plot
spectraMz = nothing # Important for memory cleaning
GC.gc() # Trigger garbage collection
end
end
else else
warning_fr = "is not an imzML file" warning_fr = "is not an imzML file"
end end
@ -98,10 +108,6 @@ using Statistics
if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <= 1 if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <= 1
msg = "File exists, Nmass=$(Nmass) Tol=$(Tol). Please do not press the start button until confirmation" msg = "File exists, Nmass=$(Nmass) Tol=$(Tol). Please do not press the start button until confirmation"
spectra = LoadImzml(full_route) spectra = LoadImzml(full_route)
full_routeMz = split( full_route, "." )[1] * ".mzML" # Splitting the route from imzml to mzml so the plotting can work
spectraMz = LoadMzml(full_routeMz)
dims = size(spectraMz)
MicroscansMax = dims[2] # we get the total of microscans
msg = "File loaded. Please do not press the start button until confirmation" msg = "File loaded. Please do not press the start button until confirmation"
slice = GetSlice(spectra, Nmass, Tol) slice = GetSlice(spectra, Nmass, Tol)
if triqProb != 0 # if we have TrIQ if triqProb != 0 # if we have TrIQ
@ -124,9 +130,6 @@ using Statistics
msgimg = "image with the Nmass of $(Int(Nmass))" msgimg = "image with the Nmass of $(Int(Nmass))"
end end
msg = "The file has been created inside the 'public' folder of the app" msg = "The file has been created inside the 'public' folder of the app"
# traceSpectra = PlotlyBase.scatter(x = spectraMz[1, 1], y = spectraMz[2, 1], mode="lines+markers")
traceSpectra = PlotlyBase.scatter(x = mean(spectraMz, dims=1), y = mean(spectraMz, dims=2), mode="lines+markers")
plotdata = [traceSpectra] # we add the data of spectra to the plot
else else
msg = "File does not exist or a parameter was not well inputted" msg = "File does not exist or a parameter was not well inputted"
end end
@ -199,3 +202,4 @@ in the UI.
@private table = DataFrame(a = 1:10, b = 10:19, c = 20:29) @private table = DataFrame(a = 1:10, b = 10:19, c = 20:29)
=# =#