jminnier / startapp Goto Github PK

though it will still download.

Hello STARTapp team,

I am using the Shiny Transcriptome Analysis Resource webTool, available at

https://kcvi.shinyapps.io/START/#dataformats

It's the best tool that I have come across to analyze transcriptome data. Thanks for such a valuable webtool.

I need a small help with this app. I have made the PCA plot using this webtool. If I directly copy the PCA made on the website by right clicking and saving it as image the resolution is very low. The journals are not accepting this image, is there a better way to either derive or download a high resolution PCA plot using this tool.

My knowledge with R studio is very limited and I ma not being able to run this on there. SO my only option is using webtool.

I would really appriciate a quick response as I am have submitted my paper to the journal but they want a high resolution image asap.

Thanks in advance.

Regards

Shwetank, Ph.D.
Prof. Aron Lukacher's Lab,
Dept of Microbiology and Immunology,
Penn State College of Medicine
Hershey, PA 17033
Lab number : 717 531 6340

I tried following the installation instructions. The app works and I can upload csv data, but when I goto Analysis Plots, I get "Error: non-character argument". I even tried the example csv data, with the same result. Please advise.

This is the stack trace in the console:

Warning: Error in strsplit: non-character argument
Stack trace (innermost first):
87: strsplit
86: do.call
85: rna_volcanoplot [fun-analysisres.R#97]
84: eval [server-analysisres.R#76]
83: eval
82: withProgress
81: "plotly"::"ggplotly" [server-analysisres.R#67]
80: func
79: origRenderFunc
78: output$volcanoplot
3: runApp
2: runUrl
1: shiny::runGitHub

Hi,
when I press the submit button the app crashes and it complains:
[1] "server-sampleplots-update-samples"
Warning: Error in [: subscript out of bounds
94: extract_count_data [fun-input-analyze-data.R#30]
93: analyze_expression_data [fun-input-analyze-data.R#94]
89: eventReactiveHandler [server-inputdata.R#122]
45: analyzeDataReactive
44: [server-filterdata.R#56]
1: runApp

My input format is according to what has been described in the instructions. Is it because I have zero in some replicates.

Hi

I am trying to run this app and am running into some trouble when i input the example data (exampleanalysisres_short.csv). My R Studio session just freezes. I am running it on a google chrome browser rather than the R-studio "browser", where it just kills it!

Since the file does not have p-vals, but rather adjp-vals, i am just using the same values from the files for both the inputs. Is this causing the freeze up?

Once i submit the files, it just greys over and i get a little "analyzing data .."
Any help would be appreciated

Thanks

Error below:
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] data.table_1.11.6 colourpicker_1.0 readr_1.1.1 heatmaply_0.15.2
[5] viridis_0.5.1 viridisLite_0.3.0 scales_1.0.0 NMF_0.21.0
[9] Biobase_2.40.0 BiocGenerics_0.26.0 cluster_2.0.7-1 rngtools_1.3.1
[13] pkgmaker_0.27 registry_0.5 markdown_0.8 plotly_4.8.0
[17] shinyBS_0.61 pheatmap_1.0.10 RColorBrewer_1.1-2 edgeR_3.22.4
[21] limma_3.36.5 DT_0.4 tidyr_0.8.1 dplyr_0.7.6
[25] ggvis_0.4.3 gplots_3.0.1 ggthemes_4.0.1 ggplot2_3.0.0
[29] reshape2_1.4.3 shiny_1.1.0

loaded via a namespace (and not attached):
[1] bitops_1.0-6 webshot_0.5.0 doParallel_1.0.14 httr_1.3.1
[5] prabclus_2.2-6 tools_3.5.1 R6_2.2.2 KernSmooth_2.23-15
[9] lazyeval_0.2.1 colorspace_1.3-2 trimcluster_0.1-2.1 nnet_7.3-12
[13] withr_2.1.2 tidyselect_0.2.4 gridExtra_2.3 compiler_3.5.1
[17] TSP_1.1-6 diptest_0.75-7 caTools_1.17.1.1 DEoptimR_1.0-8
[21] mvtnorm_1.0-8 robustbase_0.93-3 stringr_1.3.1 digest_0.6.17
[25] pkgconfig_2.0.2 htmltools_0.3.6 bibtex_0.4.2 htmlwidgets_1.2
[29] rlang_0.2.2 rstudioapi_0.7 BiocInstaller_1.30.0 bindr_0.1.1
[33] jsonlite_1.5 crosstalk_1.0.0 mclust_5.4.1 gtools_3.8.1
[37] dendextend_1.8.0 magrittr_1.5 modeltools_0.2-22 Rcpp_0.12.18
[41] munsell_0.5.0 stringi_1.2.4 whisker_0.3-2 yaml_2.2.0
[45] MASS_7.3-50 flexmix_2.3-14 plyr_1.8.4 grid_3.5.1
[49] gdata_2.18.0 promises_1.0.1 crayon_1.3.4 miniUI_0.1.1.1
[53] lattice_0.20-35 hms_0.4.2 locfit_1.5-9.1 pillar_1.3.0
[57] fpc_2.1-11.1 codetools_0.2-15 stats4_3.5.1 glue_1.3.0
[61] gclus_1.3.1 httpuv_1.4.5 foreach_1.4.4 gtable_0.2.0
[65] purrr_0.2.5 kernlab_0.9-27 assertthat_0.2.0 gridBase_0.4-7
[69] mime_0.5 xtable_1.8-3 later_0.7.5 class_7.3-14
[73] seriation_1.2-3 tibble_1.4.2 iterators_1.0.10 bindrcpp_0.2.2
[1] "inputting data"
Parsed with column specification:
cols(
Geneid = col_character(),
MGIsymbol = col_character(),
group1_1 = col_integer(),
group1_2 = col_integer(),
group1_3 = col_integer(),
group2_1 = col_integer(),
group2_2 = col_integer(),
group2_3 = col_integer(),
group3_1 = col_integer(),
group3_2 = col_integer(),
group3_3 = col_integer()
)
[1] "uploaded mousecounts data"
[1] "server-datafilter-update-filters"
[1] "analysisCountDataReactive"
[1] "server-datafilter-update-tests"
[1] "server-datafilter-update-expr"
[1] "server-dotplot-update"
[1] "server-heatmap-update"
[1] "server-samplegroupplots-update-yname"
[1] "server-samplegroupplots-update-groups"
[1] "server-sampleplots-update-samples"
[1] "server-analysisres-update"
[1] "drawing volcano plot"
[1] "drawing scatterplot"
[1] "inputting data"
Parsed with column specification:
cols(
Geneid = col_character(),
MGIsymbol = col_character(),
group1_1 = col_integer(),
group1_2 = col_integer(),
group1_3 = col_integer(),
group2_1 = col_integer(),
group2_2 = col_integer(),
group2_3 = col_integer(),
group3_1 = col_integer(),
group3_2 = col_integer(),
group3_3 = col_integer()
)
[1] "uploaded mousecounts data"
[1] "server-datafilter-update-filters"
[1] "analysisCountDataReactive"
[1] "server-datafilter-update-tests"
[1] "server-datafilter-update-expr"
[1] "server-dotplot-update"
[1] "server-heatmap-update"
[1] "server-samplegroupplots-update-yname"
[1] "server-samplegroupplots-update-groups"
[1] "server-sampleplots-update-samples"
[1] "server-analysisres-update"
[1] "drawing volcano plot"
[1] "drawing scatterplot"
[1] "inputting data"
[1] "server-datafilter-update-tests"
[1] "server-datafilter-update-expr"
[1] "server-sampleplots-update-samples"
[1] "server-datafilter-update-tests"
[1] "server-datafilter-update-expr"
[1] "server-sampleplots-update-samples"
[1] "updating analyzed data choices"
[1] "inputting data"
Parsed with column specification:
cols(
.default = col_double(),
Geneid = col_character(),
MGIsymbol = col_character()
)
See spec(...) for full column specifications.
[1] "uploaded seqdata"
[1] "server-analysisres-update"
[1] "analysisCountDataReactive"
Warning in if (input == "") { :
the condition has length > 1 and only the first element will be used
[1] "Num genes kept after removing empty geneids: 100 of 100"
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Joining, by = c("unique_id", "test")
Joining, by = c("unique_id", "test")
Joining, by = "sampleid"
Warning: Column sampleid joining character vector and factor, coercing into character vector
[1] "drawing volcano plot"
[1] "drawing scatterplot"
[1] "server-datafilter-update-filters"
[1] "server-datafilter-update-tests"
Warning in max(tmpfc, na.rm = T) :
no non-missing arguments to max; returning -Inf
[1] "server-datafilter-update-expr"
Warning: Error in FUN: only defined on a data frame with all numeric variables
50: stop
49: FUN
48: lapply
47: Summary.data.frame
46: [server-filterdata.R#77]
3: runApp
2: runUrl
1: shiny::runGitHub
[1] "server-sampleplots-update-samples"
[1] "server-dotplot-update"
[1] "server-heatmap-update"
[1] "server-samplegroupplots-update-yname"
[1] "server-samplegroupplots-update-groups"

We noticed that the Rdata file produced from the current version is different from the previous version. However, when the saved Rdata file generated from the current version is uploaded to the same current version crashes the application.

Hello,

This is a great tool, and I use it in an assignment for a bioinformatics class I teach; however, this past week several student and myself are unable to load the website from https://kcvi.shinyapps.io/START/. It just hangs and says "Please Wait".

Hello,
I am operating the STARTapp, using the function of Upload Data. An error occurs whenever the group columns is more than 18. thanks

error message

Hello,
I have the raw read counts and I generated the boxplots with your application on NASQAR. The boxplots look beautiful, however, I don't see option to add statistics or p values for the purpose of statistical differentiation between two groups.

Could you please help me to find a way to add statistics?

a comment by Les K said that this fixes and issue which makes me think it's the whole numbers (0s should be fine):

I tried a modification of the input data file and now the edgeR analysis works fine.
Namely, I made sure all the numbers were whole, no decimal places, and also added 1 to all numbers to get rid of zero values. I did both so I don’t know if one of the changes alone solved the problem.

hello,

I tried following the installation instructions. The app works and I can upload csv data, but when I goto Analysis Plots, I get Warning: Error in ggfun("create_layout"): unused argument (plot$coordinates). The example csv data, has the same result. Please advise.

Warning: Error in ggfun("create_layout"): unused argument (plot$coordinates)
Stack trace (innermost first):
93: gg2list
92: ggplotly.ggplot
91: ggplotly
90: plotly_build
89: plotly_build.gg
88: plotly_build
87: rna_scatterplot [fun-analysisres.R#196]
86: eval [server-analysisres.R#108]
85: eval
84: withProgress
83: "plotly"::"ggplotly" [server-analysisres.R#105]
82: func
81: origRenderFunc
80: output$scatterplot
3: runApp
2: runUrl
1: shiny::runGitHub

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Many thanks

a request to add tSNE plots as well as PCA plots

Hello,
during the filterdata step, I can not filter the expression value by count, it goes directly to log2cpm_voom.
I can not select count.

Thanks,

Mohamed