How to plot a table with multiple columns as a box plot

ruudoe · June 19, 2021, 3:34pm

Hello all. I am trying to plot a box plot with the Trinucleotide as the x axis (so 64 trinucleotides on the x axis) and the frequency of each trinucleotide in each of 6 samples then color code the plot according to the sample. This is a snippet of the table and the code I have so far.

library(tidyverse)
library(readxl)

marte <- read_xlsx("TrinucleotideFrequency06182021.xlsx")
marte <- gather (marte, "xzl.mmu.C57.testis.wt.adult.40S_crosslink.rep1+rept1.RPF.trimmed.gz.x_rRNA.x_hairpin.mm10v1.unique.+jxn.bed13.40S.sense.hybrid.utr3.1up.5end.PNLDC1.rep1.bed6", "xzl.mmu.C57.testis.wt.adult.40S_crosslink.rep2+rept2.RPF.R1.trimmed.gz.x_rRNA.x_hairpin.mm10v1.unique.+jxn.bed13.40S.sense.hybrid.utr3.1up.5end.PNLDC1.rep1.bed6", "xzl.mmu.C57.testis.wt.adult.40S_crosslink.rep3+rept3.RPF.R1.trimmed.gz.x_rRNA.x_hairpin.mm10v1.unique.+jxn.bed13.40S.sense.hybrid.utr3.1up.5end.PNLDC1.rep1.bed6", "xzl.mmu.C57.testis.wt.adult.80S_crosslink.rep1+rept1.RPF.trimmed.gz.x_rRNA.x_hairpin.mm10v1.unique.+jxn.bed13.RPF.sense.hybrid.utr3.1up.5end.PNLDC1.rep1.bed6", "xzl.mmu.C57.testis.wt.adult.80S_crosslink.rep2+rept2.RPF.R1.trimmed.gz.x_rRNA.x_hairpin.mm10v1.unique.+jxn.bed13.RPF.sense.hybrid.utr3.1up.5end.PNLDC1.rep1.bed6", "xzl.mmu.C57.testis.wt.adult.80S_crosslink.rep3+rept3.RPF.R1.trimmed.gz.x_rRNA.x_hairpin.mm10v1.unique.+jxn.bed13.RPF.sense.hybrid.utr3.1up.5end.PNLDC1.rep1.bed6",key="gene", value="value")
marte$gene <- as.factor(marte$Trinucleotide)  
marte$group <- as.factor(marte$gene)

ggplot(marte, aes(x = gene, y = value, color = group)) +
  geom_boxplot()

ruudoe · June 19, 2021, 3:37pm

This is what I am looking to produce

jrkrideau · June 20, 2021, 2:45pm

We need more information and reproducible example (reprex)

FAQ: How to do a minimal reproducible example ( reprex ) for beginners Guides & FAQs

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

system · July 11, 2021, 2:45pm

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