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Old 02-24-2016, 11:18 AM   #1
cbaudo
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Location: Missouri

Join Date: Jan 2013
Posts: 21
Default Modify cummeRbund plots in R studio: color, error bar width

Hello everyone,

I would like to reduce the horizontal length of the whiskers on the error bars on my expression plots, modify the color on my bar plots to black, and remove the quant type beneath the bar plot (currently says OK). I've attached photos of the plots. This link shows how the cummerbund package generates the plots, but I'm not savvy enough to figure out what to do next:https://github.com/Bioconductor-mirr...-CuffFeature.R

My scripts are:

cuff<-readCufflinks()
myGeneId<-"123456"
myGeneCuff<-getGene(Cuff,myGeneId)
gl.repCuff<-expressionPlot(myGeneCuff,replicates=TRUE)
gb.repCuff<-expressionBarplot(myGeneCuff,replicates=T)

For anyone wondering I've figured out how to modify the X and Y axis labels, remove the gray background, remove the legend, change the x axis data series name, change the blue line colour to black, remove grid lines, remove facet labels, and change title:

#Modify X and Y axis labels
gl.repCuff = gl.repCuff + labs(x = "X axis Title", y = "FPKM")

#Remove gray background
gl.repCuff = gl.repCuff + theme_bw(base_size=12)

#remove legend
gl.repCuff = gl.repCuff + theme(legend.position ='none')

#change x axis data series names
gl.repCuff = gl.repCuff + scale_x_discrete(labels=c("1" = "Hi","2" = "Hello","3" ="-Ciao", "4"= "-Adios","5" = "Bye" ))

#change blue line colour to black
gl.repCuff = gl.repCuff + scale_colour_manual(values=c("black"))

#remove grid lines
gl.repCuff= gl.repCuff + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

#remove facet labels
gl.repCuff = gl.repCuff + theme(strip.background = element_blank(), strip.text.x = element_blank())

#change title
gl.repCuff = gl.repCuff + ggtitle("Gene name")
Attached Images
File Type: jpg Errorbar_width.jpg (27.8 KB, 9 views)
File Type: jpg ColorandQuantType.jpg (23.5 KB, 11 views)
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cummerbund, cummerbund plots, r studio, rna seq

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