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  • 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 Files

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