3 Y-axes with 3 different elements

KScott — Wed, 26 Nov 2025 14:39:23 GMT

I'm trying to recreate this GC metric chart from Picard in JMP but am having trouble figuring out how to get 3 different Y-axes that all have different elements. Here is the graph I am trying to make:

This is as far as I have gotten. I added the base quality to the y axis and then moved it to the right to get two Y-axes but can't figure out how to add in the red histogram as well.

I've attached the data with the script I have so far. I'd prefer a non-coding answer if possible and am using JMP 19. Thanks so much for your help!

Re: 3 Y-axes with 3 different elements

jthi — Wed, 26 Nov 2025 15:24:42 GMT

Create range 0-1 from your windows at GC%

Add that new column to your Y-axis.

Add bar chart to your graph and disable variables from points/bar accordingly

Graph Builder(
	Size(730, 719),
	Show Control Panel(0),
	Variables(
		X(:GC% of 100 base windows),
		Y(:Mean base quality, Side("Right")),
		Y(:Fraction of normalized coverage, Position(1)),
		Y(:"Range Scale[Windows at GC%]"n, Position(1))
	),
	Elements(
		Points(X, Y(2), Legend(16)),
		Line(X, Y(1), Legend(18)),
		Bar(X, Y(3), Legend(29))
	),
	SendToReport(
		Dispatch({}, "GC% of 100 base windows", ScaleBox,
			{Min(-2.43663303909206), Add Ref Line(50, "Solid", "Black", "", 1)}
		),
		Dispatch({}, "Fraction of normalized coverage", ScaleBox,
			{Format("Fixed Dec", 12, 1), Min(-0.0597014925373134), Max(2), Inc(0.5),
			Minor Ticks(1), Add Ref Line(1, "Solid", "Black", "", 1)}
		),
		Dispatch({}, "Mean base quality", ScaleBox,
			{Format("Best", 12), Min(-1.21054871739173), Max(40.0924512083527),
			Inc(10), Minor Ticks(1)}
		),
		Dispatch({}, "400", ScaleBox,
			{Legend Model(
				16,
				Type Properties(0, "Marker", {Line Color(5), Marker("Circle")}),
				Properties(
					0,
					{Line Color(5), Marker("Circle")},
					Item ID("Fraction of normalized coverage", 1)
				),
				Properties(
					-1,
					{Line Color(5), Marker("Circle")},
					Item ID("Range Scale[Windows at GC%]", 1)
				),
				Properties(
					-1,
					{Line Color(5), Marker("Circle")},
					Item ID("Normalized_Coverage", 1)
				),
				Properties(-1, {Fill Color(35)}, Item ID("WINDOWS", 1)),
				Properties(
					-1,
					{Line Color(5), Marker("Circle")},
					Item ID("NORMALIZED_COVERAGE", 1)
				),
				Properties(
					-1,
					{Line Color(5), Marker("Circle")},
					Item ID("Windows at GC%", 1)
				)
			), Legend Model(
				18,
				Type Properties(0, "H Line", {Line Color(4)}),
				Properties(0, {Line Color(4)}, Item ID("Mean base quality", 1)),
				Properties(-1, {Line Color(4)}, Item ID("Base_Quality", 1))
			)}
		)
	)
);

Or you could add two y-axis and use Parallel Y Axes

and similarly tinker with enable/disable variables until you get what you wish

Re: 3 Y-axes with 3 different elements

KScott — Wed, 26 Nov 2025 15:47:36 GMT

Perfect, thank you!

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3 Y-axes with 3 different elements

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Re: 3 Y-axes with 3 different elements