different legends from two different data.frames

[Assa Yeroslaviz]

I have two data frames :

  TXCHROM log2FoldChange.mRNA        ID.miRNA log2FoldChange.miRNA
1    chr9          -1.0119426  mmu-miR-15a-5p           -0.2725025
2    chr9          -1.0119426  mmu-miR-30e-5p            0.2304548
4   chr14          -1.6593072  mmu-miR-15a-5p           -0.2725025
5    chr7           0.3779362  mmu-miR-19b-3p            0.4693430
6    chr7           0.3779362    mmu-miR-9-5p           -0.6406830
8    chr3          -0.4443476 mmu-miR-181a-5p           -0.2239107
and
> head(target_miRNA_chr)
              miRNA TXCHROM log2FoldChange.mRNA
276  mmu-miR-21a-5p   chr11           2.6221773
221  mmu-miR-19b-3p    chrX           0.9185626
458  mmu-miR-19b-3p   chr14           0.9185626
434  mmu-miR-221-3p    chrX           0.7513653
87  mmu-miR-145a-5p   chr18           0.3724231
207  mmu-miR-34c-5p    chr9           0.3277572


This is the script I sue to plot both data.frames into one plot.
ggplot(data=target_exp, mapping = aes(x=as.factor(TXCHROM), y=log2FoldChange.mRNA)) +
  scale_shape_manual(name = "miRNA targets", values = c(1:25)) +
  geom_point(data=target_exp, aes(size=3, colour=log2FoldChange.miRNA, shape=as.factor(ID.miRNA))) +
  geom_hline(y=log2(2), size=0.3, linetype="dashed")+
  geom_hline(y=-log2(2), size=0.3, linetype="dashed") +
  scale_colour_gradient2(name = "log2FC", low="blue", mid="grey", high="red") +
  geom_text(aes(label=label_gene), size=4, hjust=0.4, vjust=1, colour="black") +
  ggtitle(paste(sampleID, " DEmiRNAs and their corresponding targets mRNA", sep="")) +
  xlab("chromosommal position") + ylab("log2 FC target mRNA") +
  # thispart adds the miRAN names to the plot in red and map them to the chromosomal localtions found in the script 1.plotmiRNA.R
  geom_point(data=target_miRNA_chr, mapping=aes(y=log2FoldChange.mRNA), colour="red", size=5) +
  geom_text(data =target_miRNA_chr, aes(label=miRNA), size=4, hjust=0.4, vjust=1, colour="red", guied=FALSE) +
  scale_size(name="miRNA")

It all works well (see attached image), except the last commend. I would like to change the size, colour and shape in the legend of the second data.frame (miRNA). I am not really sure, why it shows me the number 3 in the legend, but I would like to have no name, the dot should be in size 5 and in a red colour.

I have tried adding the parameters size, colour and shape, but I get the error message that the parameters are not known.
I have tried to do it with the guide() command, but I am not able to tell ggplot to use it only for the second data.frame (target_miRNA_chr).

Has anyone has a suggestion how I can manipulate only a specific part of the legend?

thanks

Assa

[Hadley Wickham]

Look closely at this line:

geom_point(data=target_exp, aes(size=3, colour=log2FoldChange.miRNA, shape=as.factor(ID.miRNA)))

Hadley

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[Assa Yeroslaviz]

Thanks Hadley,

now I know why I have the number 3 in the legend.

How do I add the second genom_point data to the legend?
I can't add any scale_shape* or scale_colour_* anymore. How can I tell guied() what  I want to do?

Assa

[Assa Yeroslaviz]

Ok,

I have solved the problem by using this line:

guides(size=guide_legend(title="miRNA", override.aes = list(colour = "red"), label.theme = element_blank()))

I'm not sure, if there is a more elegant way of doing it, but it works for me now.

What I don't understand is what would have happens if I have two separate elements of type size i would have want to put in the legend. Would it be possible at all?

My question is - Is there a way to tell the guides() or the theme() command exactly which of my data sets (data.frame) in my case i wuld like to add to the legend and in what way I would like to do it?