could not generate interactive figures.

[weiliuyuan]

Hi,

I am trying to plot the interactive figs by following the introduction. However, I can only generate non-interactive plots but not the interactive ones. Could you please help me with this issue.

Many thanks!

My sessioninfo:

R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods
[10] base

other attached packages: [1] bindrcpp_0.2.2 scatterplot3d_0.3-41 rgl_0.100.19 plot3D_1.1.1
[5] GSEABase_1.44.0 graph_1.60.0 annotate_1.58.0 XML_3.98-1.11
[9] DOSE_3.6.1 org.Hs.eg.db_3.7.0 AnnotationDbi_1.44.0 IRanges_2.14.10
[13] S4Vectors_0.18.3 Biobase_2.40.0 BiocGenerics_0.26.0 circlize_0.4.6
[17] clusterProfiler_3.10.1 ReactomePA_1.26.0 ComplexHeatmap_1.18.1 Rtsne_0.13
[21] umap_0.2.2.0 iCellR_0.99.0 plotly_4.9.0 ggplot2_3.0.0
[25] plyr_1.8.4 dplyr_0.7.6 readxl_1.1.0 readr_1.1.1

[rezakj]

Hi, you need to put interactive = TRUE and give it a name like out.name = "tSNE_2D_clusters"

Example:

cluster.plot(my.obj, plot.type = "tsne", interactive = T, out.name = "tSNE_2D_clusters")

Hope this is helpful.

Reza

[weiliuyuan]

Hi Reza, Many thanks for the reply. i have set interactive = TRUE and followed the tutorial exactly. Tried both in mac and ubuntu 18.04 and i still could not generate an interactive plot.

Wei

[rezakj]

What is the error you get?

Your session looks fine, but you have a lot of attached packages maybe there is a conflict somewhere. Try opening a new R session and if you have saved the iCellR object do the following and send me the error if you get any.

library(iCellR) load("my.obj.Robj") cluster.plot(my.obj, plot.type = "tsne", interactive = T, out.name = "tSNE_2D_clusters")

Hope this works!

` R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.4

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] iCellR_0.99.0 plotly_4.9.0 ggplot2_3.1.1

loaded via a namespace (and not attached): [1] umap_0.2.0.0 Rcpp_1.0.1 later_0.8.0 [4] pillar_1.3.1 compiler_3.5.3 RColorBrewer_1.1-2 [7] plyr_1.8.4 ggpubr_0.2 tools_3.5.3 [10] digest_0.6.18 jsonlite_1.6 Rtsne_0.15 [13] tibble_2.1.1 gtable_0.3.0 viridisLite_0.3.0 [16] lattice_0.20-38 pkgconfig_2.0.2 rlang_0.3.4 [19] Matrix_1.2-17 shiny_1.3.2 crosstalk_1.0.0 [22] yaml_2.2.0 ggrepel_0.8.0 gridExtra_2.3 [25] withr_2.1.2 dplyr_0.8.0.1 httr_1.4.0 [28] htmlwidgets_1.3 scatterplot3d_0.3-41 grid_3.5.3 [31] tidyselect_0.2.5 reshape_0.8.8 reticulate_1.12 [34] glue_1.3.1 data.table_1.12.2 R6_2.4.0 [37] pheatmap_1.0.12 tidyr_0.8.3 purrr_0.3.2 [40] magrittr_1.5 promises_1.0.1 scales_1.0.0 [43] htmltools_0.3.6 assertthat_0.2.1 NbClust_3.0 [46] xtable_1.8-4 mime_0.6 colorspace_1.4-1 [49] httpuv_1.5.1 labeling_0.3 lazyeval_0.2.2 [52] munsell_0.5.0 crayon_1.3.4 `

Reza

[weiliuyuan]

Hi, i just update my R and Rstudio. Now i have got all of the interactive plots! Thank you so much for the help and also this fantastic package!

Many thanks! Wei