raivokolde/gosummaries

gosummaries's Issues

Domain names have changed in g:Profiler output

Hi Raivo,

I couldn't run gosummaries for KEGG and Reactome annotations until I realized that the annotation domain names for these databases have changed from "ke" and "re" to "keg" and "rea", respectively, in g:Profiler output. Currently, the gosummaries function documentation lists the former two names as the values for the go_branches argument. Could you please update the documentation to include the new domain names as go_branches values?

Best regards,
Mario

Issues with gosummaries

Hello,

I'm trying to run GOsummaries in RStudio and am following the GOSummaries basics PDF from bioconductor; however, when calling gosummaries on the gene list I made, I get the following error:

"Error in function (type, msg, asError = TRUE) : Server aborted the SSL handshake"

The full traceback is:
8. fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition")))
7. function (type, msg, asError = TRUE) { if (!is.character(type)) { i = match(type, CURLcodeValues) ...
6. .postForm(curl, .opts, .params, style)
5. RCurl::postForm(my_url, .opts = gp_globals$rcurl_opts, .params = query_params)
4. gProfileR::gprofiler(query = gl, organism = organism, ordered_query = ordered_query, max_set_size = max_set_size, hier_filtering = hier_filtering, max_p_value = max_p_value, ...)
3. annotate.gosummaries(res, organism = organism, go_branches = go_branches, max_p_value = max_p_value, min_set_size = min_set_size, max_set_size = max_set_size, max_signif = max_signif, ordered_query = ordered_query, hier_filtering = hier_filtering, ...)
2. gosummaries.default(gl)

1. gosummaries(gl)

Here is the R code I am running (gene lists greatly simplified):
genes1 <- c("FBgn0040736", "FBgn0035715")
genes2 <- c("FBgn0266974","FBgn0267978")
gl = list(List = list(genes1, genes2))
gs = gosummaries(gl)

Any advice would be appreciated, thanks!

Unsupproted SSL protocol version

Hi,
I am new to R and just installed GOsummaries to run an analysis on GO terms in RStudio. While running I got this error

 Error in function (type, msg, asError = TRUE)  : 
  Unsupported SSL protocol version

I am trying to run a GO term analysis on a query list compared to a background list loades as a two list into gosummaries.

The complete script looks like this:

QueryList<-as.list(read.table("NSvsS_selected_sign.txt"))
BckGrdList<-as.list(read.table("FirstGene_allGenes.txt"))
GeneList<-list(List=list(QueryList,BckGrdList))
gs<-gosummaries(GeneList, 
                organism = "mmusculus",
                go_branches = c("BP","CC","MF","ke","re")
                )

I include both files.
NSvsS_selected_sign.txt
FirstGene_allGenes.txt

Any help on solving this will be appreciated. Thanks in advance.

Error in data.frame(Query = NA, gpr) : arguments imply differing number of rows: 1, 0

Hi there! Hi @raivokolde !

I get

Error in data.frame(Query = NA, gpr) : 
  arguments imply differing number of rows: 1, 0

Calls: gosummaries ... gosummaries.default -> annotate.gosummaries -> data.frame

executing

library(GOsummaries)
genes_arabid =  read.table("DE_genes_arabid.list", header = FALSE)
genes_arabid_summary = gosummaries(genes_arabid)
plot(genes_arabid_summary , fontsize = 8, filename = "genes_arabid_summary.pdf")

on attached DE_genes_arabid.list.zip

Any help would be very appreciated.
Thanks and best regards.

max_p_value

HI Raivo,

I have been using GOsummaries and really like the functionality. Thanks for the work.
One thing I tried to play around is the p-value legend: the default for max is 1 and I would like to change it to a smaller value. I thought max_p_value would do the work but it didn't. Using the code chunk number 6 and 7 as an example:

wcd1 = data.frame(Term = c("KLF1", "KLF2", "POU5F1"), Score = c(0.05, 0.001, 0.0001))
wcd2 = data.frame(Term = c("CD8", "CD248", "CCL5"), Score = c(0.02, 0.005, 0.00001))
gs = gosummaries(wc_data = list(Results1 = wcd1, Results2 = wcd2),max_p_value = 0.001)
plot(gs)

I didn't see any difference by adding the max_p_value option. Is this expected?
Also, would you mind sharing if it's possible to custom the legend for p-value?
Many thanks.

Best,
Chia-Yi

error for plot(gs)

Hi there,

since a couple of days I have a problem with GOsummaries, so that I can't plot the gs object using plot(gs).
The error I get is:

Error in mapply(child_vp, vp_name = vpname(x$layout), t = x$layout$t, :
zero-length inputs cannot be mixed with those of non-zero length

Even if I just follow this example, I get the error when I run the last command:

genes1 = c("203485_at", "209469_at", "209470_s_at", "203999_at", "205358_at", "203130_s_at",
           "210222_s_at", "202508_s_at", "203001_s_at", "207957_s_at", "203540_at", "203000_at", "219619_at", "221805_at", "214046_at", "213135_at", "203889_at", "209990_s_at", "210016_at", "202507_s_at", "209839_at", "204953_at", "209167_at", "209685_s_at",  "211276_at", "202391_at", "205591_at", "201313_at")
genes2 = c("201890_at", "202503_s_at", "204170_s_at", "201291_s_at", "202589_at", "218499_at",
           "209773_s_at", "204026_s_at", "216237_s_at", "202546_at", "218883_s_at", "204285_s_at",
           "208659_at", "201292_at", "201664_at")

gl1 = list(List1 = genes1,  List2 = genes2) 

gs1 = gosummaries(gl1)
plot(gs1, fontsize = 8)

Output:

plot(gs1, fontsize = 8)
Error in mapply(child_vp, vp_name = vpname(x$layout), t = x$layout$t, :
zero-length inputs cannot be mixed with those of non-zero length

Any ideas what I am doing wrong here? It was running perfectly fine until a couple of days ago.

Thanks in advance
satz

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] GOsummaries_2.4.1 Rcpp_0.12.3

loaded via a namespace (and not attached):
[1] bitops_1.0-6 grid_3.2.3 plyr_1.8.3 gtable_0.2.0 magrittr_1.5 scales_0.4.0 ggplot2_2.1.0 stringi_1.0-1
[9] reshape2_1.4.1 limma_3.26.8 labeling_0.3 tools_3.2.3 stringr_1.0.0 munsell_0.4.3 RCurl_1.95-4.8 gProfileR_0.5.3
[17] colorspace_1.2-6

World cloud not showing

Hi,
I was checking your GOsummaries package to visualize some GO data.
I've tried to run the example in the go summaries help page. When I plot the data only the horizontal bar appears without the world cloud. It looks like the gProfileR is failing, because if I try a simple call to gProfileR on a gene list, I'm not able to retrieve any data. By the way, my internet connection is working fine.
Thanks.
m.

This is the code I've used:

#GOsummaries
genes1 = c("203485_at", "209469_at", "209470_s_at", "203999_at", "205358_at", "203130_s_at",
           "210222_s_at", "202508_s_at", "203001_s_at", "207957_s_at", "203540_at", "203000_at", "219619_at", "221805_at", "214046_at", "213135_at", "203889_at", "209990_s_at", "210016_at", "202507_s_at", "209839_at", "204953_at", "209167_at", "209685_s_at",  "211276_at", "202391_at", "205591_at", "201313_at")
genes2 = c("201890_at", "202503_s_at", "204170_s_at", "201291_s_at", "202589_at", "218499_at",
           "209773_s_at", "204026_s_at", "216237_s_at", "202546_at", "218883_s_at", "204285_s_at",
           "208659_at", "201292_at", "201664_at")

gl1 = list(List1 = genes1,  List2 = genes2) 

gs1 = gosummaries(gl1)
plot(gs1, fontsize = 8)

#gProfiler
gprofiler(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")

gProfiler output

[1] query.number significant p.value term.size query.size
[6] overlap.size precision recall term.id domain
[11] subgraph.number term.name relative.depth intersection
<0 rows> (or 0-length row.names)

This are the session info:
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocInstaller_1.14.3 GOsummaries_1.1 Rcpp_0.11.3 ggplot2_1.0.0

loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.4 gProfileR_0.5 grid_3.1.1 gtable_0.1.2
[6] labeling_0.3 limma_3.20.9 MASS_7.3-35 munsell_0.4.2 plyr_1.8.1
[11] proto_0.3-10 RCurl_1.95-4.3 reshape2_1.4 scales_0.2.4 stringr_0.6.2
[16] tools_3.1.1