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[Bioc-devel] Use set.seed inside function

Kasper Daniel Hansen

Tue, Nov 30, 2021 5:06 AM

Martin's suggestion is the way to go. For display purposes, you basically
never want random colors, you almost always want to select distinct colors
and there are principled ways of doing that.

Best,
Kasper

On Tue, Nov 30, 2021 at 6:59 AM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote:

Check out grDevices::hcl.pals (also
https://www.zeileis.org/papers/Zeileis+Hornik+Murrell-2009.pdf) or the
RColorBrewer package (also https://colorbrewer2.org) for principled
selection of colors. Sounds like you're interested in 'qualitative' color
palletes.

Martin Morgan

?On 11/29/21, 4:23 PM, "Bioc-devel on behalf of Meng Chen" <
bioc-devel-bounces at r-project.org on behalf of mengchen18 at gmail.com> wrote:

    Thanks. I think it may work in theory, generating "enough" distinct
colors
    is fairly easy. Then the problem will be how to find a subset of
colors of
    size n, and the selected colors are still most distinguishable. I
think I
    will do this with my eyes if no other methods, a tedious job.
    But at least for my curiosity, I still want to know if there are other
ways
    to achieve this. I feel like 80% of people who use the
distinctColorPallete
    function actually don't need the "random" feature :) Thanks.

    On Mon, Nov 29, 2021 at 9:39 PM James W. MacDonald <jmacdon at uw.edu>
wrote:

    > It appears that you don't actually want random colors, but instead

you

    > want the same colors each time. Why not just generate the vector of

'random

    > distinct colors' one time and save the vector of colors?
    >
    > -----Original Message-----
    > From: Bioc-devel <bioc-devel-bounces at r-project.org> On Behalf Of

Meng Chen

    > Sent: Monday, November 29, 2021 3:21 PM
    > To: bioc-devel at r-project.org
    > Subject: [Bioc-devel] Use set.seed inside function
    >
    > Dear BioC team and developers,
    >
    > I am using BiocCheck to check my package, it returns a warning:
    > " Remove set.seed usage in R code"
    >
    > I am using "set.seed" inside my functions, before calling function
    > distinctColorPalette (randomcoloR package) in order to generate
    > reproducible "random distinct colors". So what would be the best

practice

    > to solve this warning? I think 1. use set.seed and don't change

anything.

    > 2. use the set.seed function, but include something like below

inside the

    > function *gl.seed <- .Random.seed* *on.exit(assign(".Random.seed",

gl.seed,

    > envir = .GlobalEnv))* 3. use some other functions for the purpose
    >
    > Any suggestions will be appreciated. Thanks.
    > --
    > Best Regards,
    > Chen
    >
    >         [[alternative HTML version deleted]]
    >
    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel
    >


    --
    Best Regards,
    Chen

        [[alternative HTML version deleted]]

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Best,
Kasper

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Thread (7 messages)

Meng Chen Use set.seed inside function Nov 29 James W. MacDonald Use set.seed inside function Nov 29 Meng Chen Use set.seed inside function Nov 29 Henrik Bengtsson Use set.seed inside function Nov 29 Meng, Chen Use set.seed inside function Nov 29 Martin Morgan Use set.seed inside function Nov 30 Kasper Daniel Hansen Use set.seed inside function Nov 30