changing x axis scale using ggplot

Question

I am using ggplot library to make MAPLOT, where I want x-axis to have scale as 1,100,10000

My data looks like this(few lines)

gene    baseMean    log2FoldChange  lfcSE   stat    pvalue  padj    genename    threshold
ENSG00000223972 0.575771350800225   0.0412219472008923  3.00480558248345    0.0137186736610169  0.989054425422109   NA  DDX11L1 non_sig
ENSG00000227232 638.915585716581    0.0759771312187909  0.265826656683689   0.285814568661551   0.77502014921445    0.925602441205682   WASH7P  non_sig
ENSG00000238009 0.732676980883345   1.70580495308195    2.88536344691496    0.591192404168632   0.554391511600533   NA  RP11-34P13.7    sig
ENSG00000233750 0.665119914806497   1.43662798114606    2.40334694948042    0.597761376673745   0.549999165399301   NA  CICP27  non_sig
ENSG00000237683 1.61059299708066    1.32385867730769    1.59103144187764    0.832075748135656   0.405366189814378   NA  AL627309.1  non_sig
ENSG00000268903 0.53805903280028    1.11220672347871    3.09943388409949    0.358841893413014   0.719713370602976   NA  RP11-34P13.15   non_sig
ENSG00000241860 6.36716721142452    1.00072051754609    0.952066011135871   1.0511041312694 0.293210766884749   0.62978967383262    RP11-34P13.13   non_sig
ENSG00000228463 3.16284935240728    2.539009793132  1.21049386749042    2.09749909629516    0.0359494170864793  0.184551759280715   AP006222.2  non_sig
ENSG00000237094 3.57505447485535    -0.402759405190994  0.989965477248915   -0.406841869183409  0.684124133143038   0.887865190354194   RP4-669L17.10   non_sig

I used the following R code:

df <- read.table("test.txt",header=TRUE,sep="\t")
ggplot(df,aes(x=baseMean,y=log2FoldChange)) + geom_point(aes(col=threshold),size=1,shape=20) + ylim(-15,15)+
  scale_color_manual(values=c("gray70", "red"), name="threshold")+
  scale_x_continuous(trans = 'log10') + geom_hline(yintercept = 0,linetype="dashed",color="red")+ xlab("mean of normalized counts")+
  ggtitle("MAPLOT")+theme_classic()

When I use log10 in scale_x_continuous as argument I get 10,1000,100000 as labels on x axis. Is there a way I can get 1,100,10000 as x-axis?

Thanks

You could try setting the x axis breaks to what you want them to be with breaks in scale_x_continuous(). — aosmith
I tried doing this scale_x_continuous(breaks=c(1,100,10000)), but the graph looks squished. I want x axis to be on log 10 scale starting with 1 and not 10 — user3138373

Andrew Lavers Andrew Lavers · Accepted Answer · 2018-11-20T23:09:46

df <- read.table(text = "
gene    baseMean    log2FoldChange  lfcSE   stat    pvalue  padj    genename    threshold
ENSG00000223972 0.575771350800225   0.0412219472008923  3.00480558248345    0.0137186736610169  0.989054425422109   NA  DDX11L1 non_sig
ENSG00000227232 638.915585716581    0.0759771312187909  0.265826656683689   0.285814568661551   0.77502014921445    0.925602441205682   WASH7P  non_sig
ENSG00000238009 0.732676980883345   1.70580495308195    2.88536344691496    0.591192404168632   0.554391511600533   NA  RP11-34P13.7    sig
ENSG00000233750 0.665119914806497   1.43662798114606    2.40334694948042    0.597761376673745   0.549999165399301   NA  CICP27  non_sig
ENSG00000237683 1.61059299708066    1.32385867730769    1.59103144187764    0.832075748135656   0.405366189814378   NA  AL627309.1  non_sig
ENSG00000268903 0.53805903280028    1.11220672347871    3.09943388409949    0.358841893413014   0.719713370602976   NA  RP11-34P13.15   non_sig
ENSG00000241860 6.36716721142452    1.00072051754609    0.952066011135871   1.0511041312694 0.293210766884749   0.62978967383262    RP11-34P13.13   non_sig
ENSG00000228463 3.16284935240728    2.539009793132  1.21049386749042    2.09749909629516    0.0359494170864793  0.184551759280715   AP006222.2  non_sig
ENSG00000237094 3.57505447485535    -0.402759405190994  0.989965477248915   -0.406841869183409  0.684124133143038   0.887865190354194   RP4-669L17.10   non_sig
", 
  header = TRUE)

library(ggplot2)
ggplot(df, aes(x = baseMean, y = log2FoldChange)) + 
  geom_point(aes(col = threshold), size = 1, shape = 20) + 
  ylim(-15, 15) + 
  scale_color_manual(values = c("gray70", "red"), name = "threshold") + 
  scale_x_continuous(trans = "log10", breaks = c(1, 100, 10000), limits = c(NA, 10000)) + 
  geom_hline(yintercept = 0, linetype = "dashed",color = "red") + 
  xlab("mean of normalized counts") + ggtitle("MAPLOT") + 

 theme_classic()

changing x axis scale using ggplot

1 Answers