Holcombe:Plotting - Revision history

Alex O. Holcombe: /* polishing plots */

Alex O. Holcombe — Wed, 23 Mar 2011 22:47:53 GMT

polishing plots

←Older revision		Revision as of 22:47, 23 March 2011
Line 53:		Line 53:
	grid.gedit("GRID.text",gp=gpar(fontfamily="mono"))		grid.gedit("GRID.text",gp=gpar(fontfamily="mono"))
	#Call this after you have produced your original plot.		#Call this after you have produced your original plot.
		+
		+	p+opts(axis.title.x=theme_text(vjust=1)) #for some reason this changes the size of the axis label
		+
		+	p+opts(axis.text.x=theme_text(hjust=0.1)) #for some reason this seems to displace horizontally the ticks labels
		+
	ok		ok

Alex O. Holcombe: /* polishing plots */

Alex O. Holcombe — Sun, 13 Mar 2011 04:33:54 GMT

polishing plots

←Older revision		Revision as of 04:33, 13 March 2011
Line 49:		Line 49:
	#turn off grid		#turn off grid
	p+ opts(panel.grid.major=theme_blank(), panel.grid.minor=theme_blank())		p+ opts(panel.grid.major=theme_blank(), panel.grid.minor=theme_blank())
		+
		+	#change font. You can set the font of the labels produced by geom_text with grid.gedit:
		+	grid.gedit("GRID.text",gp=gpar(fontfamily="mono"))
		+	#Call this after you have produced your original plot.
	ok		ok

Alex O. Holcombe: /* polishing plots */

Alex O. Holcombe — Sun, 13 Mar 2011 04:18:28 GMT

polishing plots

←Older revision		Revision as of 04:18, 13 March 2011
Line 43:		Line 43:
	p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )		p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )
	p+opts(legend.key=theme_rect(fill=NULL,colour="white"))		p+opts(legend.key=theme_rect(fill=NULL,colour="white"))
		+
	#remove shading of facet_grid labels and lines around them, for better post-production editing		#remove shading of facet_grid labels and lines around them, for better post-production editing
-	q+ opts(strip.background = theme_rect(colour = 'white', fill=NULL))	+	p+ opts(strip.background = theme_rect(colour = 'white', fill=NULL))
		+
		+	#turn off grid
		+	p+ opts(panel.grid.major=theme_blank(), panel.grid.minor=theme_blank())
	ok		ok

Alex O. Holcombe: /* polishing plots */

Alex O. Holcombe — Sat, 12 Mar 2011 22:28:05 GMT

polishing plots

←Older revision		Revision as of 22:28, 12 March 2011
Line 43:		Line 43:
	p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )		p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )
	p+opts(legend.key=theme_rect(fill=NULL,colour="white"))		p+opts(legend.key=theme_rect(fill=NULL,colour="white"))
		+	#remove shading of facet_grid labels and lines around them, for better post-production editing
		+	q+ opts(strip.background = theme_rect(colour = 'white', fill=NULL))
	ok		ok

Alex O. Holcombe: /* polishing plots */

Alex O. Holcombe — Sat, 12 Mar 2011 22:23:30 GMT

polishing plots

←Older revision		Revision as of 22:23, 12 March 2011
Line 42:		Line 42:
	theme_bw() #see associated list of options		theme_bw() #see associated list of options
	p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )		p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )
-	p+opts(legend.key=theme_rect(fill=~~"blue"~~,colour="white"))	+	p+opts(legend.key=theme_rect(fill=NULL,colour="white"))
		+	ok

Alex O. Holcombe: /* polishing plots */

Alex O. Holcombe — Sat, 12 Mar 2011 22:22:50 GMT

polishing plots

←Older revision		Revision as of 22:22, 12 March 2011
Line 42:		Line 42:
	theme_bw() #see associated list of options		theme_bw() #see associated list of options
	p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )		p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )
		+	p+opts(legend.key=theme_rect(fill="blue",colour="white"))

Alex O. Holcombe at 09:23, 12 March 2011

Alex O. Holcombe — Sat, 12 Mar 2011 09:23:07 GMT

←Older revision		Revision as of 09:23, 12 March 2011
Line 36:		Line 36:

	pvalsCIs$subject<-factor(pvalsCIs$subject,levels=c("AH","SM","SYL","WYC","DL")) #levels(pvalsCIs$subject)		pvalsCIs$subject<-factor(pvalsCIs$subject,levels=c("AH","SM","SYL","WYC","DL")) #levels(pvalsCIs$subject)
		+
		+	===polishing plots===
		+	See Chapter 8 of the ggplot book
		+	p+ theme_bw() #changes all options to those of theme_bw
		+	theme_bw() #see associated list of options
		+	p + opts( axis.text.x= theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "grey50", hjust = 1, angle = 90) )

Alex O. Holcombe at 22:59, 10 March 2011

Alex O. Holcombe — Thu, 10 Mar 2011 22:59:49 GMT

←Older revision		Revision as of 22:59, 10 March 2011
Line 13:		Line 13:
	str(g) #gives you everything!		str(g) #gives you everything!
	summary(g) #gives a summary		summary(g) #gives a summary
		+	options(g) #lists the options
	last_plot() #refreshes the last plot and returns the struct		last_plot() #refreshes the last plot and returns the struct

Alex O. Holcombe: New page: {{Template:Holcombe}} Good advice on [http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatGraphCourse/graphscourse.pdf graph choice, from human perceptual standpoint] by Frank Harrell ==...

Alex O. Holcombe — Thu, 10 Mar 2011 22:58:14 GMT

New page: {{Template:Holcombe}} Good advice on [http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatGraphCourse/graphscourse.pdf graph choice, from human perceptual standpoint] by Frank Harrell ==...

New page

{{Template:Holcombe}}

Good advice on [http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatGraphCourse/graphscourse.pdf graph choice, from human perceptual standpoint] by Frank Harrell

==ggplot2==

In the lab we usually use the R package, [http://had.co.nz/ggplot2/ ggplot2], for graphs. Ask Sarah about the ggplot2 book.

For custom colour schemes, the [http://research.stowers-institute.org/efg/R/Color/Chart/ Chart of R Colors] is a helpful resource. The table with named colours is most useful.

ggplot2 tips:
#where 'g' is your ggplot object
str(g) #gives you everything!
summary(g) #gives a summary
last_plot() #refreshes the last plot and returns the struct

p=p+scale_y_continuous(breaks=c(0,0.5,1),minor_breaks=c(.25,.75)) #changing axis breaks
p=p+opts(title="one-behind errors")
p=p+xlab('relative phase')

opts(panel.grid.minor = theme_blank())+

last_plot() + opts(panel.grid.minor = theme_line(colour = "black") )

facet_grid(.~subject) # rows~columns

g<-g+stat_summary(fun.y=mean,geom="point",position="jitter") #getting jitter to work when you're collapsing across other variables with stat_summary

g=g+ stat_smooth(method="glm",family="binomial",fullrange=TRUE) #adds logistic smoother to plot
#it's impossible to extract the function fits however because they're fit on the fly
#how can I fit an arbitrary function, like a psychometric function, e.g. cumulative gaussian with chance rate and lapse rate? Logistic is restricted to 0->1

order used for scale mapping (color, etc.) is perhaps the order of the levels property of the vector. This gives bizarre results because R's sort(unique(x)) default does not alphabetize strings. Getting things to appear in a graph or something the way you want may require reordering the 'levels' of a factor, like this to put DL as the last subject to be graphed:

pvalsCIs$subject<-factor(pvalsCIs$subject,levels=c("AH","SM","SYL","WYC","DL")) #levels(pvalsCIs$subject)