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I have several character vectors of genes containing names of the species in which they're found, and I made an UpSetR plot to show the number of species in common across genes. Now I'd like to do the opposite: Plotting the number of genes in common across species, yet I don't know how to do it.

\n\n

Example of what I have:

\n\n

gene1 <- c(\"Panda\", \"Dog\", \"Chicken\")\ngene2 <- c(\"Human\", \"Panda\", \"Dog\")\ngene3 <- c(\"Human\", \"Panda\", \"Chicken\")  \n...#About 20+ genes with 100+ species each\n

\n\n

Example of what I would like to have as a result:

\n\n

Panda <- c(\"gene1\", \"gene2\", \"gene3\")\nDog <- c(\"gene1\", \"gene2\")\nHuman <- c(\"gene2\", \"gene3\")\nChicken <- c(\"gene1\", \"gene3\")\n...  \n

\n\n

I know it is conceptually easy, yet logistically more complicated. Can anyone give me a clue?

\n\n

Thank you!

\n"}}],["$","hr",null,{}],["$","div",null,{"className":"h3","children":["Solution ",["$","li",null,{"className":"h3 fa fa-arrow-down"}]]}],["$","hr",null,{}],["$","$L12",null,{}],["$","div",null,{"dangerouslySetInnerHTML":{"__html":"

You can use unstack from base R:

\n\n

unstack(stack(mget(ls(pattern=\"gene\"))),ind~values)\n$Chicken\n[1] \"gene1\" \"gene3\"\n\n$Dog\n[1] \"gene1\" \"gene2\"\n\n$Human\n[1] \"gene2\" \"gene3\"\n\n$Panda\n[1] \"gene1\" \"gene2\" \"gene3\"\n

\n\n

You can end up listing this to the environment by list2env function

\n\n

Breakdown:

\n\n

 l = mget(ls(pattern=\"gene\"))#get all the genes in a list\n m = unstack(stack(l),ind~values)# Stack them, then unstack with the required formula\n m\n$Chicken\n[1] \"gene1\" \"gene3\"\n\n$Dog\n[1] \"gene1\" \"gene2\"\n\n$Human\n[1] \"gene2\" \"gene3\"\n\n$Panda\n[1] \"gene1\" \"gene2\" \"gene3\"\n\n list2env(m,.GlobalEnv)\n Dog\n [1] \"gene1\" \"gene2\"\n

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