topic Re: Bar and Errorbar Colors for Forest Plot? in Discussions

Bar and Errorbar Colors for Forest Plot?

pmroz — Wed, 28 Feb 2018 15:01:22 GMT

I'm creating forest plots and have come up with two styles:

I'm trying to control the color of the bars, points and error bars through row colors:

My question is why aren't the solid bars and the error bars in the desired color?

dt = New Table( "Forest Plot", Add Rows( 5 ), 
	New Column( "EVENT_NAME", Character( 20 ), "Nominal",
		Set Values( {"AAAAAAA", "BBBBBBB", "CCCCCCC", "DDDDDDD", "EEEEEEE"} ) ),
	New Column( "DISPROP025", Numeric, "Continuous", Format( "Fixed Dec", 16, 2 ),
		Set Values(
			[5.3766744840813, 1.28687381477736, 5.96303490967794, 1.55531597890029, 2.34164191312678] ) ),
	New Column( "DISPROP", Numeric, "Continuous", Format( "Fixed Dec", 16, 2 ),
		Set Values(
			[5.76756983251198, 1.49287821887835, 7.02941951612351, 3.83591362397761, 2.62194430908125] ) ),
	New Column( "DISPROP975", Numeric, "Continuous", Format( "Fixed Dec", 16, 2 ),
		Set Values(
			[6.06935482201811, 1.66251397924122, 7.91895228410917, 6.92389142535734, 2.84619058478479] ) ),
	New Column( "Alert", Character, "Nominal",
		Formula( If( :DISPROP025 > 1 & :DISPROP > 2, "Y", "N" ) ) ),
	Set Row States( [13568, 13056, 13568, 13568, 13568] )
);

// Bars + central point
dt << Graph Builder(
	Show Control Panel( 0 ),
	Variables(
		X( :DISPROP025 ),
		X( :DISPROP, Position( 1 ) ),
		X( :DISPROP975, Position( 1 ) ),
		Y( :EVENT_NAME )
	),
	Elements(
		Bar( X( 1 ), X( 3 ), Y, Legend( 9 ), Bar Style( "Range" ) ),
		Points( X( 2 ), Y, Legend( 10 ), Jitter( 0 ) )
	),
	SendToReport(
		Dispatch( {}, "DISPROP025", ScaleBox,
			{Min( 0 ), Add Ref Line( 1, "Dotted", "Dark Red", "", 2 ),
			Label Row( Show Major Grid( 1 ) )}
		),
		Dispatch( {}, "EVENT_NAME", ScaleBox, {Label Row( Show Major Grid( 1 ) )} ),
		Dispatch( {}, "X title", TextEditBox, {Set Text( "Disproportionality" )} ),
		Dispatch( {}, "Y title", TextEditBox, {Set Text( "PT" )} )
	)
);

// Error bars
dt << Graph Builder(
	Show Control Panel( 0 ),
	Variables(
		X( :DISPROP025 ),
		X( :DISPROP, Position( 1 ) ),
		X( :DISPROP975, Position( 1 ) ),
		Y( :EVENT_NAME )
	),
	Elements(
		Bar( X( 1 ), X( 3 ), Y, Legend( 9 ), Bar Style( "Interval" ) ),
		Points( X( 2 ), Y, Legend( 10 ), Jitter( 0 ) )
	),
	SendToReport(
		Dispatch( {}, "DISPROP025", ScaleBox,
			{Min( 0 ), Add Ref Line( 1, "Dotted", "Dark Red", "", 2 ),
			Label Row( Show Major Grid( 1 ) )}
		),
		Dispatch( {}, "EVENT_NAME", ScaleBox, {Label Row( Show Major Grid( 1 ) )} ),
		Dispatch( {}, "X title", TextEditBox, {Set Text( "Disproportionality" )} ),
		Dispatch( {}, "Y title", TextEditBox, {Set Text( "PT" )} )
	)
);

Re: Bar and Errorbar Colors for Forest Plot?

Chris_Kirchberg — Wed, 28 Feb 2018 15:07:09 GMT

Hi,

Have you taken a look at Richard Zink's add-in on forest plots?

https://community.jmp.com/t5/JMP-Add-Ins/Forest-Plot-Add-In/ta-p/23977

Since the Add-in is esentially a zip file, you can rename the file extension to .zip and unzip it. There you can see his JSL and maybe use some of that.

Chris

Re: Bar and Errorbar Colors for Forest Plot?

Chris_Kirchberg — Wed, 28 Feb 2018 15:21:11 GMT

You might have to use the Alert variable to color. This works on the bar graph but not the error bar graph.The Error Bar color is controlled by the legend color. Not sure how to script different colors for different error bars.

Re: Bar and Errorbar Colors for Forest Plot?

Chris_Kirchberg — Wed, 28 Feb 2018 15:25:30 GMT

Wait, I found a way. If you open the control panel and go to the section the says bar at the bottom, there will be a varialbe section. Open it and check all variables. a point will appear where you want it. Remove the points element from teh graph. Then use Alert variable for overlay.

So the script would look something like this


Graph Builder(
	Size( 606, 564 ),
	Variables(
		X( :DISPROP025 ),
		X( :DISPROP, Position( 1 ) ),
		X( :DISPROP975, Position( 1 ) ),
		Y( :EVENT_NAME ),
		Overlay( :Alert )
	),
	Elements(
		Bar( X( 1 ), X( 3 ), X( 2 ), Y, Legend( 9 ), Bar Style( "Interval" ) )
	),
	SendToReport(
		Dispatch(
			{},
			"DISPROP025",
			ScaleBox,
			{Add Ref Line( 1, "Dotted", "Dark Red", "", 2 ),
			Label Row( Show Major Grid( 1 ) )}
		),
		Dispatch( {}, "EVENT_NAME", ScaleBox, {Label Row( Show Major Grid( 1 ) )} ),
		Dispatch(
			{},
			"400",
			ScaleBox,
			{Legend Model(
				9,
				Properties( 0, {Line Color( 6 )} ),
				Properties( 1, {Marker( "Dot" )} ),
				Properties( 2, {Line Color( -5682409 )} ),
				Properties( 3, {Marker( "Dot" )} )
			)}
		),
		Dispatch( {}, "X title", TextEditBox, {Set Text( "Disproportionality" )} ),
		Dispatch( {}, "Y title", TextEditBox, {Set Text( "PT" )} )
	)
);

Re: Bar and Errorbar Colors for Forest Plot?

pmroz — Wed, 28 Feb 2018 15:34:36 GMT

Thanks Chris. I did a search for Forest Plots and Richard's very nice addin didn't show up. I like your coding solution as well.

Re: Bar and Errorbar Colors for Forest Plot?

pmroz — Wed, 28 Feb 2018 15:47:57 GMT

One more puzzler - when I drag my Alert column into the Overlay role I can control the colors nicely. However the points are on the horizontal lines but the error bars aren't. Any way to correct this? If I drag Alert onto the Color role there is no "jitter", but then I can't set the color of the error bars.

Re: Bar and Errorbar Colors for Forest Plot?

Chris_Kirchberg — Wed, 28 Feb 2018 16:04:42 GMT

The Key to using overlay is to not have the Points graph element added. Click on the Points Icont at the top to turn it off. Then Bar options/discolsure box at the bottom left, put a check next to the variable DISPROP. Points will not be added inline with the error bar.

Re: Bar and Errorbar Colors for Forest Plot?

pmroz — Wed, 28 Feb 2018 19:14:57 GMT

Still no joy. It appears that when there is a mix of Y and N alerts, the error bars are offset from the gridlines.

Here's the code:


Graph Builder(
	Size( 726, 451 ),
	Show Control Panel( 0 ),
	Show Legend( 0 ),
	Variables(
		X( :DISPROP025 ),
		X( :DISPROP975, Position( 1 ) ),
		X( :DISPROP, Position( 1 ) ),
		Y( :EVENT_NAME ),
		Overlay( :Alert )
	),
	Elements(
		Bar( X( 1 ), X( 2 ), X( 3 ), Y, Legend( 8 ), Bar Style( "Interval" ) )
	),
	SendToReport(
		Dispatch( {}, "DISPROP025", ScaleBox,
			{Min( 0 ), Add Ref Line( 1, "Dotted", "Dark Red", "", 1 ),
			Label Row( Show Major Grid( 1 ) )}
		),
		Dispatch( {}, "EVENT_NAME", ScaleBox, {Label Row( Show Major Grid( 1 ) )} ),
		Dispatch( {}, "400", ScaleBox,
			{Legend Model(
				8,
				Properties( 0, {Line Color( 51 ), Line Width( 2 )} ),
				Properties( 1, {Line Color( 51 ), Marker( "FilledCircle" )} ),
				Properties( 2, {Line Color( 53 ), Line Width( 2 )} ),
				Properties( 3, {Line Color( 53 ), Marker( "FilledCircle" )} )
			)}
		)
	)
);

Re: Bar and Errorbar Colors for Forest Plot?

Chris_Kirchberg — Wed, 28 Feb 2018 20:49:36 GMT

Well, darn it. Another way is to stack the DISPROP columns into one and make the value column (called data in the below script) continuous. Then use this script


Graph Builder(
	Size( 992, 630 ),
	Show Control Panel( 0 ),
	Variables( X( :Data ), Y( :EVENT_NAME ), Overlay( :Alert ) ),
	Elements(
		Points(
			X,
			Y,
			Legend( 5 ),
			Jitter( 0 ),
			Summary Statistic( "Median" ),
			Error Bars( "Range" )
		)
	),
	SendToReport(
		Dispatch( {}, "Data", ScaleBox, {Label Row( Show Major Grid( 1 ) )} ),
		Dispatch( {}, "EVENT_NAME", ScaleBox, {Label Row( Show Major Grid( 1 ) )} )
	)
);

Its close, but there is still somthing a little off about the grid line and the data points using overlay

Re: Bar and Errorbar Colors for Forest Plot?

pmroz — Wed, 28 Feb 2018 21:03:37 GMT

That is a clever solution that is "close enough for government work". I thickened the lines to a width of 2 and the slight offset is not noticeable. Thanks Chris!