Final visualisation step

[yashsondhi]

Hi, I got the volcano plot working, but the heatmap portion is not showing up. I am mapping RNA seq reads to a genome.

This is the output of the script when I run it only using R.
(rasflow) [yashsondhi@login4 RASflow]$ Rscript scripts/visualize.R output/test_25_march/moth/genome/dea/countGroup output/test_25_march/moth/genome/dea/DEA output/test_25_march/moth/genome/dea/visualization
Loading required package: plotscale
hash-3.0.1 provided by Decision Patterns

Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:hash’:

values, values<-

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘AnnotationDbi’

The following objects are masked from ‘package:hash’:

keys, keys<-

Loading required package: ggplot2
Loading required package: ggrepel
Querying chunk 1
Querying chunk 2
Querying chunk 3
Querying chunk 4
Querying chunk 5
Querying chunk 6
Querying chunk 7
Querying chunk 8
Querying chunk 9
Querying chunk 10
Querying chunk 11
Querying chunk 12
Querying chunk 13
Querying chunk 14
Querying chunk 15
Querying chunk 16
Finished
Pass returnall=TRUE to return lists of duplicate or missing query terms.
Error in .request.get(mygene, paste("/query/", sep = ""), params) :
Request returned unexpected status code:
Response [http://mygene.info/v3/query/?fields=symbol]
Date: 2020-04-01 15:38
Status: 400
Content-Type: application/json; charset=UTF-8
Size: 65 B
{
"success": false,
"error": "Missing required parameters."
Calls: plot.volcano.heatmap ... query -> query -> query -> .request.get -> .request.get
Execution halted

[zhxiaokang]

Hi, the error indicates that the problem happens when using the package mygene. It is used twice in scripts/visualize.R: line 57 gene.symbol.dea.all <- queryMany(gene.id.dea, scopes = 'ensembl.gene', fields = 'symbol') and line 106 gene.symbol.norm.table <- queryMany(gene.id.norm.table, scopes = 'ensembl.gene', fields = 'symbol')$symbol. As you said that volcanoplot is plotted (in line 88), so the error must come from line 106.

Reading the code in scripts/visualize.R from line 90 to line 106, it's clear that the problem is the normalized count table: control_gene_norm.tsv and treat_gene_norm.tsv. Could you check them out (maybe compare them with the example data data/example/dea/countGroup/oil_control_gene_norm.tsv and data/example/dea/countGroup/oil_low_gene_norm.tsv)?

[yashsondhi]

Hi,
I compared the files and found that there is an addition of the word gene: in front of the gene id if I remove all of these it runs. I will work on removing it in R, I could fix it easily in python, but if you have any suggestions on doing it in the script, that would be helpful. Thank you

[zhxiaokang]

I see. The extra word "gene" before the gene ID confused the program. But the design of RASflow shouldn't add that extra word. So I can't figure out why that is happening without taking a look at your code and data. Otherwise, if a little bit of manual work (removing it manually) is OK for you, then it's fine.

[yashsondhi]

I tried to look at the code too and could not figure out why it was being added, I can just call a small python script to do it, thanks for the help. Manually worked too since it is only 4 files. I can run the script after sea and before visualisation. Thanks

…

On Sun, Apr 19, 2020 at 4:50 AM xkzhang ***@***.***> wrote: I see. The extra word "gene" before the gene ID confused the program. But the design of RASflow shouldn't add that extra word. So I can't figure out why that is happening without taking a look at your code and data. Otherwise, if a little bit of manual work (removing it manually) is OK for you, then it's fine. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEAELVPFAYTHR6UFWZC6KELRNK3L5ANCNFSM4LZCY47A> .

-- Yash Sondhi PhD Student Department of Biological Sciences Florida International University, Member, Titli trust www.titlitrust.org Co- editor, Moths of India www.mothsofindia.org Email: yash@ifoundbutterflies.org

[zhxiaokang]

Sounds great! I'll close the issue for now. Feel free to open it whenever it's necessary