CODEWITHSUNDEEP
rmultiple-columns
user53965
user53965

Reputation: 1

How do I plot multiple columns on the X-axis in R?

I start with a set of 100 genes that are most often found in a certain biological substance, this list is called "top100". Using MERGE I manage to get the counts for each of this 100 proteins out of this dataset for each of the samples. I want to plot the counts for each individual protein, per sample.

So basically I want a plot that shows for instance: protein: PKM and than plots for each of the samples (N=2 in this case) the counts, than I want to repeat this process for all 100 proteins in individual plots.

            row.names   Gene.Symbol     Normalised.count.(B)        Normalised.count.(A)
    1           1           A2M             46.073855                   280.736354
    2           5           ACTN4           0.000000                    10.436296
    3           8           ALDOA           39.354751                   61.574145
    4           9           ANXA1           1.919744                    1.043630
    5           13          ANXA5           8.638848                    0.000000
    6           17          BSG             5.759232                    1.043630
    7           22          CD81            1.919744                    2.087259
    8           23          CD9             2.879616                    4.174518
    9           25          CFL1            5.759232                    10.436296
    10          26          CLIC1           1.919744                    10.436296

This is 1/10 of the total list, so for each gene symbol I want both noramlised count values plotted where

X1 = gene symbol y= normalised.count.(A)

X2= gene symbol y= normalised.count.(B)

This is what I got so far to sort to the final list. 

 library("openxlsx") 
 library("dplyr")
 library("ggplot2")
 library('reshape2')
 library('gdata')

 protein_report <- read.xlsx(file.choose(), sheet=1)
 top100 <- read.xlsx(file.choose(), sheet=1)

 norm <- matchcols(protein_report,with = "Norm")
 top <- na.omit(merge(top100, protein_report[c("Gene.names",norm)], by.x="Gene.Symbol",by.y="Gene.names", all.x = T, all.y = F))

How to plot these values?

Upvotes: 0

Views: 2205

Answers (1)

nist
nist

Reputation: 1721

You could use tidyr and the gather function to first reshape the data into long format and then plot it with ggplot

library(tidyr)
library(ggplot2)

plotData <- protein_report %>% gather(type,Normalised.count,
                                      Normalised.count.A,Normalised.count.B)

ggplot(plotData,aes(x=Gene.Symbol,y=Normalised.count,color=type) + 
       geom_line()    ## For a line plot

Upvotes: 1

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