I wanted to create an accessible html page of my interactive heatmap from Interactive Complex heatmap and the following is my code; the running of app is successful but the deployment is not i get the following error from the code below
Warning: unable to access index for repository https://github.com/jokergoo/InteractiveComplexHeatmap.git/src/contrib: cannot open URL 'https://github.com/jokergoo/InteractiveComplexHeatmap.git/src/contrib/PACKAGES' Warning: unable to access index for repository https://github.com/jokergoo/ComplexHeatmap.git/src/contrib: cannot open URL 'https://github.com/jokergoo/ComplexHeatmap.git/src/contrib/PACKAGES
I understand that if i use install_github() from devtools i dont have to set the URL under options repos=() However, when i am currently unable to reinstall Interactive Complex Heatmap using install_github() due to "non zero exit status" error; therefore i am setting the direct URL for rsconnect to access.
App.R Code below:
options(repos = c("CRAN" = "https://cran.rstudio.com/", "BioC" = "https://bioconductor.org/packages/3.12/bioc/","InteractiveComplexHeatmap"="https://github.com/jokergoo/InteractiveComplexHeatmap.git","ComplexHeatmap"="https://github.com/jokergoo/ComplexHeatmap.git"))
library(ComplexHeatmap)
library(InteractiveComplexHeatmap)
library(RColorBrewer)
library(shiny)
library(rsconnect)
colAnn <- HeatmapAnnotation(df=my_sample_col,which = "col",col=genotypecolors)
rowAnn <- HeatmapAnnotation(df=mygenecol2,which = "row",col=themecolors)
heatmap=Heatmap(counts, name = "Z-score counts", col = myCol,column_title = "%s",
cluster_rows = FALSE,show_column_dend = FALSE,row_split = mygenecol2,column_split = my_sample_col,row_title_rot = 0,column_km = 1,
left_annotation = rowAnn,row_names_gp =gpar(fontsize=2))
ht=draw(heatmap)
htShiny(ht)
library(shiny)
ui = fluidPage(
InteractiveComplexHeatmapOutput()
)
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht)
}
shinyApp(ui = ui, server = server)
deployApp("C:/Users/K/Desktop/appdir/myapp")
Hope to get any advice please! I dont understand why rsconnect is unable to link to the github package source URL. I am very lost and i dont know where to edit... Please help! Thank you!
App works fine lcoally btw.
