Entering edit mode
4.2 years ago
remi.montagne91
▴
10
Hello,
I am trying to use glimma
to generate an interactive volcano plot of differentially expressed genes, found with EdgeR
.
I would like to add annotations to this plot, so that when you hover a point, you get the name of the gene. However, I get an error message every time.
Here is my code (I use shiny) :
glXYPlot(x= de.df()$logFC,
y=-log10(de.df()$FDR),
xlab="logFC",
ylab="-log(FDR)",
status=de.df()$FDR <= 0.05,
anno=as.vector(de.df()$genes))
```
de.df looks like this:
genes logFC logCPM LR PValue FDR
ENSG00000018625 CXorf56 4.731732 7.700889 21.57148 3.408840e-06 0.005551464
ENSG00000065534 SPEN 4.131256 12.597048 19.89395 8.185875e-06 0.005551464
ENSG00000007933 DNAJC11 5.340935 5.797704 19.28277 1.127190e-05 0.005551464
ENSG00000091986 CCDC80 3.829369 11.839320 18.55905 1.647217e-05 0.005551464
ENSG00000022267 C8B 3.820883 11.532498 18.43854 1.754731e-05 0.005551464
ENSG00000007908 TEAD3 5.402253 6.162232 18.41020 1.781025e-05 0.005551464
And the error I get is:
Warning: Error in checkThat: Second argument should contain the first.
I really don't understand what the problem is.
Does anyone have any idea ?
de.df()$logFC
=> the()
afterde.df
do not really make sense, do they? Parentheses after variable names indicate a function. Try removing all()
after that variable in every line of code.I use the
()
because this isshiny
code and you need it to call the result (here a dataframe) of a reactive expression.I also tried this code in a plain R script, so without the parenthesis and reactive expressions, but I have the same error so I think it's not the problem.
can you do some thing like this? (replace df with de.df and assumption is that Ensembl IDs are row names of the data frame):
column name
GeneID
is mandatory.