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Hi all,<BR>
<BR>
I am using RKward in Ubuntu for a while now. I am fascinated with the interface and the productivity.<BR>
<BR>
Currently, I am working on a large data sets where summary tables and plots are important for visualization. I managed to create table and graphs and pipe them to the output. However, I am having problems with the output settings.<BR>
<BR>
What I get:<BR>
Huge font size in TOC - <A HREF="http://imageshack.us/photo/my-images/823/rkout1.png/[">http://imageshack.us/photo/my-images/823/rkout1.png/</A><BR>
Considerable blank spaces after the title.<BR>
No control on the size of the output image.<BR>
<BR>
What I wish:<BR>
Control over each level of TOC fonts and spacings (using some sort of parameters)<BR>
Copy graphs to the output according to a certain specifications (for example 480 X 240 px) (I can create a desired graph by changing parameters within RKWard, however, when the graph is copied to output it goes to default.<BR>
<BR>
There is one last thing:<BR>
When I use the following code, I get one graph in the active window (I am copy pasting code for each variable - which is a crude way to do it, but I am not really savvy with looping mechanism yet). "Previous and next" is - grayed out. Usually when I get boxplots from a data within RKward, I get sequential outputs and I can go back and forth to look at individual plots.<BR>
[img]<A HREF="http://imageshack.us/photo/my-images/94/007kj.png/[">http://imageshack.us/photo/my-images/94/007kj.png/[</A>/img]<BR>
<BR>
[b]My RKward version:[/b]<BR>
RKWard<BR>
Version 0.5.7z+0.6.0+pre1<BR>
Using KDE Development Platform 4.7.4 (4.7.4)<BR>
<BR>
[b]Here is my kernel version[/b]<BR>
3.0.0-26-generic #43-Ubuntu SMP Tue Sep 25 17:19:22 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux<BR>
<BR>
Here is the script and demo data:<BR>
# New version of length which can handle NA's: if na.rm==T, don't count them<BR>
library(doBy)<BR>
length2 <- function (x, na.rm=FALSE) {<BR>
if (na.rm) sum(!is.na(x))<BR>
else length(x)<BR>
}<BR>
cdataNA <- summaryBy(tyr ~ spp + wat + ins, data=demo, FUN=c(length2,mean,sd), na.rm=TRUE)<BR>
# Rename column change.length to just N<BR>
names(cdataNA)[names(cdataNA)=="tyr.length2"] <- "N"<BR>
levels(cdataNA$wat) <- c(levels(cdataNA$wat), "High")<BR>
cdataNA$wat[cdataNA$wat == "Yes"] <- "High" <BR>
levels(cdataNA$wat) <- c(levels(cdataNA$wat), "Low")<BR>
cdataNA$wat[cdataNA$wat == "No"] <- "Low"<BR>
# Calculate standard error of the mean<BR>
cdataNA$tyr.SE <- cdataNA$tyr.sd / sqrt(cdataNA$N)<BR>
#Print table at output<BR>
rk.header(level = 2, "Summary table - tyr")<BR>
rk.print(cdataNA, titles = NULL, align = "left")<BR>
# Now create a barplot using ggplot2<BR>
library(ggplot2)<BR>
a <- ggplot(cdataNA, aes(x = wat, y = tyr.mean, fill = ins))<BR>
b <- a + geom_bar(stat = "identity", position = "dodge") + facet_grid (~ spp)<BR>
# Now put errorbars.<BR>
c <- b + geom_errorbar(aes(ymin=tyr.mean-tyr.SE, ymax=tyr.mean+tyr.SE), <BR>
width=.2, # Width of the error bars<BR>
position=position_dodge(.9)) + <BR>
xlab ("wat") + <BR>
ylab ("tyr (PA/PA std)")<BR>
c<BR>
rk.header("tyr:")<BR>
## Copy the displayed plot to the output:<BR>
plot (c, align = "left")<BR>
dev.copy (device = rk.graph.on)<BR>
rk.graph.off ()<BR>
<BR>
Link to demo data: [url]<A HREF="http://pastebin.com/M4iEJUPf[">http://pastebin.com/M4iEJUPf[</A>/url]<BR>
<BR>
I appreciate any help on this.<BR>
<BR>
Thanks in advance.<BR>
<BR>
Best,<BR>
Sourav<BR>
<BR>
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