degPatterns error

[wangmhan]

Hi, I tried to use degPatterns with consensusCluster = TRUE, cannot get a result but end fraction message. Does anyone know how to fix it? Thanks!

[lpantano]

Hi @wangmhan ,

Can you post the exact error you get? If you try the example in the man page, does it work?

If you paste here all the output when you run it, I may able to see what is happening.

Thanks!

[wangmhan]

Hi,

I tried the example, it also cannot work with consensusCluster = TRUE.

The code is like this: library("DEGreport")

data(humanGender) library(SummarizedExperiment) library(ggplot2) ma <- assays(humanGender)[[1]][1:100,] des <- colData(humanGender) des[["other"]] <- sample(c("a", "b"), 85, replace = TRUE) res <- degPatterns(ma, des, time="group", col = "other",consensusCluster = TRUE)

And the error report is: Working with 100 genes. end fraction Error in frame() : figure margins too large

Did I misunderstand end fraction as error? But it cannot get the plot of cluster as usual.

[lpantano]

I see, are you using R studio, this happens in general when the Panel for figures is too small. Can you try to increase the size of that panel? It is working for me.

If you are not using R studio, let me know.

Cheers

[wangmhan]

Hi, yes I am using R studio. And you are right, after increasing the size of panel, it works! Thanks a lot!

Cheers

Lorena Pantano [email protected] 于2019年8月9日周五 下午9:49写道：

I see, are you using R studio, this happens in general when the Panel for figures is too small. Can you try to increase the size of that panel? It is working for me.

If you are not using R studio, let me know.

Cheers

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lpantano/DEGreport/issues/27?email_source=notifications&email_token=AJVYTVTYSXKV2LOBIQGLUWDQDXC25A5CNFSM4IKJHGA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD37TPCA#issuecomment-520042376, or mute the thread https://github.com/notifications/unsubscribe-auth/AJVYTVROV3DUFFEX4XM5JRDQDXC25ANCNFSM4IKJHGAQ .

[FengWalker]

Hi, I tried the example, The code is like this:

library("DEGreport") data(humanGender) library(SummarizedExperiment) library(ggplot2) ma <- assays(humanGender)[[1]][1:100,] des <- colData(humanGender) des[["other"]] <- sample(c("a", "b"), 85, replace = TRUE) res <- degPatterns(ma, des, time="group", col = "other",consensusCluster = TRUE)

And the error report is: Working with 100 genes. Working with 63 genes after filtering: minc > 15 Joining, by = "merge" error: Problem with summarise() input n_genes. x could not find function "n" i Input n_genes is n(). i The error occurred in group 1: merge = "aFemale", cluster = 1, group = "Female", other = "a". Run rlang::last_error() to see where the error occurred.

and I ran rlang::last_error() with this result

rlang::last_error() <error/dplyr_error> Problem with summarise() input n_genes. x could not find function "n" i Input n_genes is n(). i The error occurred in group 1: merge = "aFemale", cluster = 1, group = "Female", other = "a". Backtrace:

1. DEGreport::degPatterns(...)
2. base::.handleSimpleError(...)
3. dplyr:::h(simpleError(msg, call)) Run rlang::last_trace() to see the full context.

[lpantano]

Hi, Thanks for reporting this. Can you tell me the version of the package and R/Bioconductor you are using?

[FengWalker]

Thanks for your reply. I run example in Rstudio Version 1.2.5033 and R version 4.0.3.
My DEGreport is version 1.25.3 and installed by remotes .

remotes::install_github("lpantano/DEGreport")

All packages were updated during the installation.

[lpantano]

Hi,

I was able to reproduce when installing from github, I am trying to fix this.

Can you trying installation directly from Bioconductor:

BiocManager::install("DEGreport")

Thanks!