How to create color range for RPKM/FPKM using R?
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8.1 years ago
Whoknows ▴ 890

Hi every body

I want to create a color range for FPKM/RPKM data using R or another software if it possible, but i don't know how to do it.

For better understanding please take a look at the photo.Thanks a lot RNA-Seq R Graphic ggplot2 gplots • 3.6k views
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I might suggest using a density plot of values instead. It will be much more informative, I suspect.

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yes i've read this kind of scale_gradient() diagram but as you see in the chart my values are discrete,

please note that i have more than 10000 FPKM/RPKM values which will be show in the diagram,

anyway thanks again,

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Err, your FPKM/RPKM values are continuous, that's why you can simply color by value and use a gradient scale, as in that image.

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BTW, you probably want to color on log2 level.

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yes of course log2, but how !!??

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The simplest way would be to just graph log2(RPKM) to begin with. Alternatively, just add that as a column to the dataframe or just perhaps even use something like colour=log2(RPKM) as an argument.

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What do you want to use the color gradient for, a heatmap?

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8.1 years ago
Whoknows ▴ 890

I offer this way if anybody expert in R please develop it

x <- data.frame(FPKM = rnorm(1000))
x$Color <- cut(x$FPKM, 256)
library(gplot)
library(ggplot2)
x$Color2 <- redgreen(256)[as.numeric(x$Color)]
ggplot(x, aes(FPKM,1,fill=Color2))+geom_bar(stat="identity")+coord_flip()
// Or use below after log2
ggplot(y, aes(FPKM,ymin=-1,ymax=1,color=Color))+
geom_linerange()+coord_flip()+theme(legend.position="none")+scale_x_log10()

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Is library(gplot) supposed to be library(gplots)? I tried the graph, and it seems like kind of an odd way to represent the data. Also I get the following error when using the code

> ggplot(y, aes(FPKM,ymin=-1,ymax=1,color=Color))+
+ geom_linerange()+coord_flip()+theme(legend.position="none")+scale_x_log10()
Error: ggplot2 doesn't know how to deal with data of class numeric


Did you copy the code exactly? I agree with the previous poster that said a histogram would be much more informative. They are fairly simple to make, just use the hist() function.

hist(x[,1])


Alternatively, you could plot the data as a line or xyplot where the cumulative percent (or actual number) of genes is on the y-axis and RPKM value (log2) is on the x-axis.