r - Error bars in ggplot in middle of bin -

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this question has answer here:

i'm trying make bar plot in ggplot 2 values each bin (fold change values rna-seq , qpcr experiments):

gene    fc  expt    se   1.02    rna-seq 0 b   2.79    rna-seq 0 c   1.63    rna-seq 0 d   0.84    rna-seq 0 e   0.81    rna-seq 0 f   1.45    rna-seq 0 g   1.27    rna-seq 0 h   1.72    rna-seq 0   2.52    rna-seq 0   0.84    qpcr    0.16 b   1.92    qpcr    0.15 c   1.14    qpcr    0.78 d   0.47    qpcr    0.76 e   0.95    qpcr    0.26 f   0.32    qpcr    0.51 g   0.92    qpcr    0.39 h   0.97    qpcr    0.61   1.73    qpcr    0.77

my rna-seq values don't have error bars. such want plot barchart with:

  • error bars extend
  • error bars q-pcr bars

i'm not sure code (or input format) going wrong:

df <- read.table("stack.txt", header=true) limits <- aes(ymax = fc + se, ymin = fc) dodge <- position_dodge(width = 0.9)  ggplot(data=df, aes(x=gene, y=fc)) + geom_errorbar(limits, position = dodge, width = 0.25) + geom_bar(aes(fill=expt),colour="black", stat="identity", position = dodge)

which produces:

enter image description here

as can see, error bars in middle of each bin, rather being onto of each bar. suggestions/comments hugely appreciated!

when add group parameter aes, desired result:

ggplot(data=df, aes(x=gene, y=fc, fill=expt, group=expt)) +   geom_bar(colour="black", stat="identity", position = position_dodge(width = 0.9)) +   geom_errorbar(aes(ymax = fc + se, ymin = fc, group=expt),                 position = position_dodge(width = 0.9), width = 0.25)

this gives:

enter image description here


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