Hi,

Your "hgnc2pfam.rdb" is completely outdated, and so all lollipops mutations don't match correctly.
It would be nice to update it, or in a more reliable and sustainable way, permit the user to query his own database or directly the Pfam website.

Otherwise, you did a nice and beautiful job to build this library !

Hope this message will reach you.

A fellow researcher.

Hi, Dr. Guo,

thank you for your helpful package. We are using it a lot and really appreciate it!

I have one question regarding the domain color: is it possible to manually specify the color of domains? E.g. I would like to color each domain of a gene red.

If it is not possible in R directly, can I change some settings in g3lollipop.js to achieve this?

HTML widgets don't get recycled when rendering g3viz plots inside a Shiny application. Please run the attached code snippet to verify its behaviour.

library(g3viz)

mutation.csv <- system.file("extdata", "ccle.csv", package = "g3viz")
selectize_values <- function(){
    return(levels(read.csv(mutation.csv, header = T)$Hugo_Symbol))
}


ui <- fluidPage(
    titlePanel("g3lollipop test"),
    sidebarLayout(
        sidebarPanel(
            selectizeInput("gene", "Elija un gen de la muestra", selectize_values())
        ),
        mainPanel(
            g3LollipopOutput("distPlot",width = "800px")
        )
    )
)

server <- function(input, output, session) {

    
    output$distPlot <- renderG3Lollipop({
    
        mutation.dat <- readMAF(mutation.csv,
                                gene.symbol.col = "Hugo_Symbol",
                                variant.class.col = "Variant_Classification",
                                protein.change.col = "amino_acid_change",
                                sep = ",")  # column-separator of csv file
        
        gene <- input$gene
        theme <- g3Lollipop.theme(theme.name = "cbioportal",
                         title.text = paste0(gene, " gene"),
                         y.axis.label = paste0("# of ", gene, " Mutations"))
        theme[['chartWidth']] <- "1600"
        
        g3Lollipop(mutation.dat,
                   gene.symbol = gene,
                   protein.change.col = "amino_acid_change",
                   plot.options = theme,
                   btn.style = "gray", 
                   output.filename = "customized_plot")
        
    })
}
shinyApp(ui = ui, server = server)

In this screenshot the unexpected behaviour is shown: after selecting two times a different gene, the second plot is created below the first one, instead of replacing it.

My current sessionInfo() is as follows:

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.1

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=es_AR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_AR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] g3viz_1.1.1 shiny_1.3.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        rstudioapi_0.10   magrittr_1.5      xtable_1.8-3      R6_2.4.0         
 [6] rlang_0.3.4       stringr_1.4.0     tools_3.6.0       packrat_0.5.0     R.oo_1.22.0      
[11] htmltools_0.3.6   yaml_2.2.0        digest_0.6.18     crayon_1.3.4      cgdsr_1.2.10     
[16] later_0.8.0       htmlwidgets_1.4   promises_1.0.1    mime_0.6          stringi_1.4.3    
[21] compiler_3.6.0    R.methodsS3_1.7.1 jsonlite_1.6      httpuv_1.5.1

Hello!

First of all, great tool! Very intuitive and easy to use. I have a quick naive question: Is it possible to save as a .png or other formats such as .pdf directly, without printing out rendered figures and having to click on the save buttons? I checked the introduction tutorial page, but I couldn't find the answer I was looking for.

Best,
Yuka

As, writen in the documation, g3viz::g3Lollipop.options(chart.width= 800) parameter can contain only numeric values that represent pixels. Would that be possible to add option for "auto", "full_width", "100%" or similar to automatically scale the chart size?

Hi!
lovely package. Is it possible to make that across different genes, the colors for the mutation classes are the same? currently, I have for some genes, yellow for missense, red for truncating, and black for inframe, but sometimes black is truncating. I would like the legend to be consistent.
thanks

Hello,

I am using readMAF to read in a csv file from the latest CCLE mutation files and noticed there were two classes that are not currently classified: Stop_Codon_Del, Stop_Codon_Ins (see warning message below).

Would it be possible to add these in the next release?

Warning message:
In mapMutationTypeToMutationClass(maf.df[, variant.class.col], mutation.type.to.class.df) :
  Unknown variant classification: Stop_Codon_Del, Stop_Codon_Ins, 

Best,
Yuka

I want to present my mutation list with G3viz. The input file is formated like example file "ccle.csv" and can be read by readMAF.

The program promotes "Error in hgnc2pfam(hgnc.symbol = gene.symbol, uniprot.id = uniprot.id) :
geneX has no uniprot mappings (wrong name or non-protein-coding gene)."

For non-human species, how can I adjust G3viz?

Is it good to run this on hg38 as well?

Hi guys, I am new to R programming. I have made my g3viz lollipop using the blue theme. I like everything about my lollipop except for the blue background. I was wondering if there is anyway to make the background white.

Thank you

Is there a way to set e.g. truncating variants to be circles (default shape) and missense to be squares, etc? It would be more friendly to color-blind people vs. relying on colors only.

Hi, Dr. Guo,

I just emailed you about the question several days ago. When I compared the lolllipop results from your nice tool, g3viz, and cBioPortal website, I found that the domain names on g3viz lollipop didn't appear as I put the mouse on them. I had saved the result plot as a html file, and used R 3.6.2 and g3viz 1.3.3.

Hope you can handle this as soon as posible to make the g3viz more user-friendly.

Fei Quan

Hello, Dr.Guo
first, thanks for developing this useful package!

In my case, I want to use 'variant allele fraction' as a y value instead of '# of mutations in gene'
is there any way to change the y position in the recent version?

thanks to read!

I'm trying to use the guide to generate plots from a tsv file. The first command for reading tsv files read my file as an empty file, i.e.: "". I'm not sure what I'm doing wrong. Could you please provide a test tsv file so I can start from there and modify it to make my input? My tsv file contains three columns: Hugo_Symbol Variant_Classification amino_acid_change

The command I used: mutation.tsv <- system.file("extdata", "myfile.tsv", package = "g3viz")

Thank you!

Hi!
Really useful package! but I can't make the g3Lollipop() function to work on a Linux-based system, (while I tried it on a MacOS based one and it works perfectly!)
The plottting area in Rstudio remains white, it only displays the buttons for saving the image, but no action happens when pressing these buttons and no error is raised at all
hgnc2pfam() on the other hand works perfectly

I've tried with R-3.6.1 and R-3.5.3, and had the same situation

Could you check what may be wrong?
Thank you very much!

This is my session info:

sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS: /opt/R/3.5.3/lib/R/lib/libRblas.so
LAPACK: /opt/R/3.5.3/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] knitr_1.26 kableExtra_1.1.0 g3viz_1.1.2

loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 pillar_1.4.2 compiler_3.5.3 R.methodsS3_1.7.1 tools_3.5.3 zeallot_0.1.0
[7] digest_0.6.22 jsonlite_1.6 evaluate_0.14 tibble_2.1.3 viridisLite_0.3.0 pkgconfig_2.0.3
[13] rlang_0.4.1 rstudioapi_0.10 yaml_2.2.0 xfun_0.11 cgdsr_1.3.0 stringr_1.4.0
[19] httr_1.4.1 xml2_1.2.2 vctrs_0.2.0 htmlwidgets_1.5.1 hms_0.5.2 webshot_0.5.1
[25] glue_1.3.1 R6_2.4.0 rmarkdown_1.16 readr_1.3.1 magrittr_1.5 backports_1.1.5
[31] scales_1.0.0 htmltools_0.4.0 rvest_0.3.5 colorspace_1.4-1 stringi_1.4.3 munsell_0.5.0
[37] crayon_1.3.4 R.oo_1.23.0

Hi -

This is Ino from the cBioPortal team. We are looking to retire cgdsr, but we see g3viz uses it quite a bit. How complex would it be to switch to using the new cBioPortalData package?

In some scenarios, the user may have a MAF already loaded into a data frame. This is the case for our workflows because MAF data is retrieved from a local database. I couldn't find an option to allow readMAF to process a data frame directly instead of relying on a file. I added this functionality but cannot create a pull request. I wonder if others might find this useful if added to the existing code:

@@ -46,24 +46,28 @@ readMAF <- function(maf.file,
                     mutation.type.to.class.df = NA,
                     sep = "\t",
                     quote = "",
+                    maf.df,
                     ...) {
-  if(missing(maf.file)){
-    stop("maf.file is missing")
+  if(missing(maf.file) & missing(maf.df)){
+    stop("maf.file and maf.dat are missing, you must provide one or the other")
   }
-
+
   # ===============================
   # TODO:
   # - check "Mutation_Status" as "Somatic"
   # ===============================
   # read data in
-  if(grepl(pattern = 'gz$', maf.file)){
-    suppressWarnings(
-      maf.df <- read.table(gzfile(description = maf.file), header = TRUE, sep = sep, quote = quote, ...)
-    )
-  } else {
-    maf.df <- read.table(maf.file, header = TRUE, sep = sep, quote = quote, ...)
+  if(missing(maf.df)){
+    if(grepl(pattern = 'gz$', maf.file)){
+      suppressWarnings(
+        maf.df <- read.table(gzfile(description = maf.file), header = TRUE, sep = sep, quote = quote, ...)
+      )
+    } else {
+      maf.df <- read.table(maf.file, header = TRUE, sep = sep, quote = quote, ...)
+    }
   }

+

Hello, I am unable to load a MAF file from my customized pipeline that is quoted with "\"", because readMAF() doesn't allow me to specify the quote argument. Looking into the readMAF.R file, I can see that the argument is used by default with a value of "". This argument should be used as a default instead, allowing users to optionally specify it just like the sep argument.

Hi,

I was trying to install the package in RStudio and get an error (please see below). I have also attached my sessionInfo(). Is there anything else that I should be doing?

thanks!

==================

install.packages("g3viz")
Installing package into ‘/Users/pankajchopra/Library/R/4.0/library’
(as ‘lib’ is unspecified)

There is a binary version available but the source version is later:
binary source needs_compilation
g3viz 1.1.4 1.1.5 FALSE

installing the source package ‘g3viz’

trying URL 'https://cran.rstudio.com/src/contrib/g3viz_1.1.5.tar.gz'
Content type 'application/x-gzip' length 1879204 bytes (1.8 MB)

downloaded 1.8 MB

• installing source package ‘g3viz’ ...
  ** package ‘g3viz’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: object ‘getDataByGenes’ is not exported by 'namespace:cBioPortalData'
  Execution halted
  ERROR: lazy loading failed for package ‘g3viz’
• removing ‘/Users/pankajchopra/Library/R/4.0/library/g3viz’
• restoring previous ‘/Users/pankajchopra/Library/R/4.0/library/g3viz’
  Warning in install.packages :
  installation of package ‘g3viz’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/wh/g8yjlv2j01xc6xs691xzt34h0000gn/T/RtmpoDQVgp/downloaded_packages’

sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] bnlearn_4.8.3 processx_3.8.1 htmltools_0.5.5

loaded via a namespace (and not attached):
[1] BiocManager_1.30.20 compiler_4.0.4 fastmap_1.1.1 cli_3.6.1 parallel_4.0.4
[6] tools_4.0.4 rstudioapi_0.14 digest_0.6.31 ps_1.7.5 rlang_1.1.1

When loading CSV data is it possible to highlight specific mutations as a seperate categories within the lollipop plot.

See below for example:

Here I went into the html output manually & changed the Mutation_class attribute for this mutation specifically- however is there a way to do this programatically within g3viz?

Additionally- is there a way to configure the appearance of specific classifications? I.e. make the "Weee - Waa" classed variants a specific colour or slightly bigger?

Loving the tool & looking forward to expanding my understanding & usage of it.