Legend for visualizeRegion/visualizeGene/visualizeProbes

[alanlamsiu]

Is there a way to add the legend (color scale) when using visualizeRegion/visualizeGene/visualizeProbes? Thanks!

[zwdzwd]

Yes, you can add it with WLegendV or WLegendH to the resulting grid objects. something like

visualizeProbes(...) + WLegendV('betas', TopRightOf())

[alanlamsiu]

Thanks for pointing to the WLegendV function. I tried it with visualizeGene() but it showed the "Error in objs[[1]] : subscript out of bounds" message. Do you think it has something to do with the betas object, which was generated by openSesame()?

[zwdzwd]

Can you try the following example?

betas <- sesameDataGet('HM450.10.TCGA.PAAD.normal')
visualizeGene('DNMT1', betas, platform='HM450') + WLegendV("betas", TopRightOf("betas"))

[alanlamsiu]

Yes, this example works fine. I noticed that there were some probes with NAs and I thought thoese might be an issue. So I removed probes with NA, however, the subscript out of bounds error still occurred. If not adding WLegendV(), the figure was generated without any issue.

[zwdzwd]

One possibility is that there is no beta value heatmap after removing the NAs. If so, yeah, the legend might be struggling to find the original color scale.

[alanlamsiu]

I would also suspect so. Below is what the heatmap looks like after removing the NAs. Yet, the "subscript out of bound" error persisted.

[zwdzwd]

OK. If you can share with me an example to reproduce this, I can troubleshoot more.

[alanlamsiu]

I extracted the beta values of 16 probes associated with the FMR1 gene as shown in this table. I tried to use this matrix as input for visualizeGene() and WLegendV() but the error message showed up on my end. Appreciate if you could look into the issue.

[zwdzwd]

can you try

betas = read_tsv("~/Downloads/test_betas.txt")
b2 = as.matrix(betas[,2:7])
rownames(b2) = betas[[1]]
visualizeGene("FMR1", b2, platform="EPIC") + WLegendV("betas", TopRightOf("betas"))

[alanlamsiu]

It works now. I guess the trick is in the data type of betas/b2. Thanks Wanding for your help.

Just a note here. It worked for me if I first saved the probes to be plotted in a variable named "betas" and then plotted it using the "betas" variable. I tried to name it as "temp_betas" but it didn't work.