[rkward-cvs] SF.net SVN: rkward:[2403] branches/release_branch_0.4.9/rkward/plugins/ plots

sjar at users.sourceforge.net sjar at users.sourceforge.net
Thu Feb 19 23:48:44 UTC 2009 

Revision: 2403
          http://rkward.svn.sourceforge.net/rkward/?rev=2403&view=rev
Author:   sjar
Date:     2009-02-19 23:48:43 +0000 (Thu, 19 Feb 2009)

Log Message:
-----------
New Feature (status: basically working but needs refinements)
* added option to show mean and standard deviation (sd) in boxplot
* colour, symbols and symbol size can be defined by the user
	> symbols for sd can be chosen independently
	> if not changed by the user they should be easily recognizable

known issues:
* GUI needs clean-up/rearrangements
* php/R-code uses points() instead of arrows() because the visual impression of a boxplot may suffer otherwise
* works only with input from RKWards table GUI or with data.frames of same length
   won't work with data.frames of different length
	# currently investigated solution is the usage of the plyr package
	Example for the plyr packge with three different data.frames:
		require(plyr)
		List <- list(data.frame(2,1,3,2,4,5), data.frame(2,3,4), data.frame(1,2,4,3,2,4,5,4,2))
		data_of_List<-do.call(rbind.fill, List)
		data_of_List
	# BUT it's not really reasonable to make the plug-in dependent of yet another package, thus open for alternative solutions (maybe loops)

Modified Paths:
--------------
    branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.php
    branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.xml

Modified: branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.php
===================================================================
--- branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.php	2009-02-19 23:23:04 UTC (rev 2402)
+++ branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.php	2009-02-19 23:48:43 UTC (rev 2403)
@@ -19,7 +19,10 @@
 	$xvarsstring = join (", ", split ("\n", getRK_val ("x")));
 	$names_mode = getRK_val ("names_mode");
 	$mean = getRK_val ("mean");
+	$pch_mean = getRK_val ("pch_mean");
 	$sd = getRK_val ("sd");
+	$pch_sd_high = getRK_val ("pch_sd_high");
+	$pch_sd_low = getRK_val ("pch_sd_low");
 	$horizontal = getRK_val ("orientation");
 	$plot_adds = getRK_val ("plotoptions.code.calculate"); //add grid and alike
 
@@ -39,21 +42,21 @@
 <?	} ?>
 try (boxplot (data_list, notch = <? getRK ("notch") ?>, outline = <? getRK("outline")?>, horizontal = <? getRK("orientation"); ?><? getRK ("plotoptions.code.printout"); ?>)) #actuall boxplot function
 <?	if (($mean == "TRUE") && ($horizontal == "TRUE")) {?>
-	try (points(1:length(data_list) ~ apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE),pch=19, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)) #calculates the mean for all data and adds a point at the corresponding position
+	try (points(1:length(data_list) ~ apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE),pch=<? echo ($pch_mean); ?>, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)) #calculates the mean for all data and adds a point at the corresponding position
 <?	} if (($mean == "TRUE") && ($horizontal == "FALSE")) {?>
-	try (points(apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE),pch=19, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)) #calculates the mean for all data and adds a point at the corresponding position
+	try (points(apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE),pch=<? echo ($pch_mean); ?>, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)) #calculates the mean for all data and adds a point at the corresponding position
 <?	}
 ?>
 <?	if (($sd == "TRUE") && ($horizontal == "FALSE")) {?>
 	sd_low <- (apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE)) - (apply(data.frame(<? echo ($xvarsstring); ?>),2,sd,na.rm = TRUE))
 	sd_high <- (apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE)) + (apply(data.frame(<? echo ($xvarsstring); ?>),2,sd,na.rm = TRUE))
-	points(sd_low,pch=3, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
-	points(sd_high,pch=3, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
+	points(sd_low,pch=<? echo ($pch_sd_low); ?>, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
+	points(sd_high,pch=<? echo ($pch_sd_high); ?>, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
 <?	} if (($sd == "TRUE") && ($horizontal == "TRUE")) {?>
 	sd_low <- (apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE)) - (apply(data.frame(<? echo ($xvarsstring); ?>),2,sd,na.rm = TRUE))
 	sd_high <- (apply(data.frame(<? echo ($xvarsstring); ?>),2,mean,na.rm = TRUE)) + (apply(data.frame(<? echo ($xvarsstring); ?>),2,sd,na.rm = TRUE))
-	points(1:length(data_list) ~ sd_low,pch=3, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
-	points(1:length(data_list) ~ sd_high,pch=3, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
+	points(1:length(data_list) ~ sd_low,pch=<? echo ($pch_sd_low); ?>, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
+	points(1:length(data_list) ~ sd_high,pch=<? echo ($pch_sd_high); ?>, cex = <? getRK ("cex_sd_mean"); ?><? getRK ("sd_mean_color.code.printout"); ?>)
 <?	}
 ?>
 <?	if (!empty ($plot_adds)) { ?>

Modified: branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.xml
===================================================================
--- branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.xml	2009-02-19 23:23:04 UTC (rev 2402)
+++ branches/release_branch_0.4.9/rkward/plugins/plots/box_plot.xml	2009-02-19 23:48:43 UTC (rev 2403)
@@ -49,8 +49,19 @@
 					<stretch/>
 				</column>
 				<column>
-					<checkbox id="mean" checked="false" value="TRUE" label="show mean" />
-					<checkbox id="sd" checked="false" value="TRUE" label="show standard deviation" />
+					<row>
+						<checkbox id="mean" checked="false" value="TRUE" label="show mean" />
+						<spinbox type="integer" id="pch_mean" label="mean symbol" initial="19"/>
+					</row>
+					<row>
+						<column>
+							<checkbox id="sd" checked="false" value="TRUE" label="show standard deviation" />
+						</column>
+						<column>
+							<spinbox type="integer" id="pch_sd_high" label="standard deviation symbol (upper)" initial="3"/>
+							<spinbox type="integer" id="pch_sd_low" label="standard deviation symbol (lower)" initial="3"/>
+						</column>
+					</row>
 					<spinbox type="real" id="cex_sd_mean" label="size" initial="1"/>
 					<embed id="sd_mean_color" component="rkward::color_chooser" label="Color"/>
 					<embed id="plotoptions" component="rkward::plot_options" as_button="true" label="Plot Options" />


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