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kimpenn / PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data
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rendering of some plot doesn't work #3

Closed aurelBZH closed 5 years ago

aurelBZH commented 6 years ago

Hi Quin, Thanks for the quick response to my previous issue. unfortunately i have another another one.
with my data and also with the example data some plot aren't rendering. I think a library doesn't work properly. I past you the content of the R console if it help you.
Warning in origRenderFunc() : Ignoring explicitly provided widget ID "29b4e0674d"; Shiny doesn't use them No trace type specified: Based on info supplied, a 'scatter3d' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter3d Warning in origRenderFunc() : Ignoring explicitly provided widget ID "29b42c9ce2da"; Shiny doesn't use them No trace type specified: Based on info supplied, a 'scatter3d' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter3d No scatter3d mode specifed: Setting the mode to markers Read more about this attribute -> https://plot.ly/r/reference/#scatter-mode Warning in origRenderFunc() : Ignoring explicitly provided widget ID "29b4478341da"; Shiny doesn't use them Warning in origRenderFunc() : Ignoring explicitly provided widget ID "29b43e2027ea"; Shiny doesn't use them Warning in origRenderFunc() : Ignoring explicitly provided widget ID "29b4163c07a7"; Shiny doesn't use them Warning in RColorBrewer::brewer.pal(N, "Set2") : minimal value for n is 3, returning requested palette with 3 different levels
expression_plot

I have some warning at the launching of the application : 1: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PIVOT’ 2: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PIVOT’ 3: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PIVOT’ 4: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PIVOT’ 5: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PIVOT’ 6: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PIVOT’ 7: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘PIVOT’ 8: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘PIVOT’ 9: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘PIVOT’ 10: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘PIVOT’ 11: replacing previous import ‘igraph::groups’ by ‘plotly::groups’ when loading ‘PIVOT’ 12: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘PIVOT’ 13: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘PIVOT’ 14: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘PIVOT’ 15: replacing previous import ‘igraph::as_data_frame’ by ‘tibble::as_data_frame’ when loading ‘PIVOT’

May be a problem of compatibility between plotly and ggplot2 ?

qinzhu commented 6 years ago

Did u try clicking a gene in the table? For the second plot, it only works when the selected column is not sample. Could u try change that to group? It is meant to show a pie chart representing the e.g. cell type composition.

aurelBZH commented 6 years ago

The second one work but the Expression Plot don't render.

qinzhu commented 6 years ago

Hmm, that's weird, as I can't reproduce the problem. Could you try update ggplot? The warnings seem fine and not related to this problem

image

aurelBZH commented 6 years ago

I have updated ggplot2 and tested other things but the bug is already present.

qinzhu commented 6 years ago

Not sure what caused this but I'll update the plotting module with some enhanced features later.

aurelBZH commented 6 years ago

I try to reinstall your application on a new virtual machine to see if i can reproduce the problem and i have the same problem. I have created a virtual machine with ubuntu 16.4 64 bit installed R 3.4.3 ( rbase and r base dev ) installed rstudio installed libcurl4-openssl-dev, libxml2-dev, libxt-dev, libcairo2-dev, libmariadb-client-lgpl-dev, libssl-dev and do the the installation of the bioconductor lib as said in the manual after the installation of pivot from github , Pivot work but the expression plot don't render.

qinzhu commented 6 years ago

Thanks for the info! May I ask what system you original run PIVOT on? Is it also Linux?

aurelBZH commented 6 years ago

yes linux mint

qinzhu commented 6 years ago

Thanks, maybe some of my later updates broke the plotting in Linux. I'll run a thorough test.