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plot.cca with optimize=TRUE and ordipointlabel in pipe #674

Merged
merged 26 commits into from
Aug 1, 2024
Merged

plot.cca with optimize=TRUE and ordipointlabel in pipe #674

merged 26 commits into from
Aug 1, 2024

Commits on Jul 19, 2024

  1. ordipointlabel can be used in a pipe ... almost 

    Arg 'add = TRUE' needs tweaking: points are currently drawn only
with 'add = FALSE'.
    @jarioksa
    jarioksa committed Jul 19, 2024
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Commits on Jul 20, 2024

  1. ordipointlabel(decorana(dune)) failed (perhaps some other, too)

    @jarioksa
    jarioksa committed Jul 20, 2024
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  2. plot.ordipointlable: message on size differences of new and original 

    10% difference in graphic device dimensions  triggers message.
mar() is not checked, but it also influences plot size.
    @jarioksa
    jarioksa committed Jul 20, 2024
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Commits on Jul 21, 2024

  1. ordipointlabel: tweak optimization rules 

    - try more times: now 64 (was 48) means that on average each
  position is tried 8 times (was 6).
- a bit more detailed and stronger penalty: now against moving
  towards origin and against corners.
    @jarioksa
    jarioksa committed Jul 21, 2024
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Commits on Jul 22, 2024

  1. ordipointlabel: do not pass dot args to ordiplot(..., type="n") 

    Triggers false warnings if using args for scores(), for instance.
    @jarioksa
    jarioksa committed Jul 22, 2024
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  2. ordipointlabel: recycle cex, font, pch, col for 'display'

    @jarioksa
    jarioksa committed Jul 22, 2024
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  3. ordipointlabel: strwidth/height do not use vector cex, font

    @jarioksa
    jarioksa committed Jul 22, 2024
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  4. ordipointlabel gains arg 'label' & labels() function to see current ones

    @jarioksa
    jarioksa committed Jul 22, 2024
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  5. ordipointlabel failed with one 'display'; default cex to standard 0.7

    @jarioksa
    jarioksa committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. ordilabel: drqwing polygons is slow - dev.hold()/dev.flush() helps

    @jarioksa
    jarioksa committed Jul 23, 2024
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  2. ordipointlabel gained arg 'bg' to draw text onnon-transparent background

    @jarioksa
    jarioksa committed Jul 23, 2024
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  3. ordipointlabel *always* draws points, even with add=TRUE

    @jarioksa
    jarioksa committed Jul 23, 2024
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  4. ordipointlabel did not set font with one 'display'

    @jarioksa
    jarioksa committed Jul 23, 2024
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  5. importFrom(grDevices, dev.hold, dev.flush)

    @jarioksa
    jarioksa committed Jul 23, 2024
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  6. ordipointlabel: default to add = TRUE when used in a pipe

    @jarioksa
    jarioksa committed Jul 23, 2024
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Commits on Jul 25, 2024

  1. ordipointlabel: adapt help to using pipes

    @jarioksa
    jarioksa committed Jul 25, 2024
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  2. text.ordiplot and hence plot.cca can optimize text locations 

    Function text.ordiplot gains arg 'optimize' to call ordipointlabel
to move text to reduce overlap, but put a point in the exact
location. Function plot.cca uses text.ordiplot and gains the same
ability. For instance, plot(cca(dune), spe.par = list(optimize=TRUE)).
    @jarioksa
    jarioksa committed Jul 25, 2024
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  3. scores.default: ignore 'display' if input is a single matrix 

    This makes easier to have programmatic use of scores() when
input parameter can be a pre-processed matrix instead of a complex
list of matrices. Earlier ordipointabel(x, display=what) failed
in text.ordiplot() when called from plot.cca().
    @jarioksa
    jarioksa committed Jul 25, 2024
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  4. ordilabel: border defaults to text colour

    @jarioksa
    jarioksa committed Jul 25, 2024
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  5. plot.cca: set explicitly cex=1 instead of assuming text/points do so

    @jarioksa
    jarioksa committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. plot.cca: fix warnings on non-graphical arg 'optimize'

    @jarioksa
    jarioksa committed Jul 26, 2024
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Commits on Jul 28, 2024

  1. text.ordiplot and hence plot.cca handle 'bg' with 'optimize'

    @jarioksa
    jarioksa committed Jul 28, 2024
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  2. plot.cca handles 'optimize = TRUE' 

    - global arg (dot argument) 'optimize = T' must be eval'ed to make
  it logical TRUE (will be symbol initially)
- add point defPointPar if pch not given by user
- message on arrows looking strange with optimize=TRUE
    @jarioksa
    jarioksa committed Jul 28, 2024
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  3. update help pages for ordipointlabel pipe and next stage of plot.cca

    @jarioksa
    jarioksa committed Jul 28, 2024
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Commits on Jul 29, 2024

  1. ordipointlabel could drop dimensions

    @jarioksa
    jarioksa committed Jul 29, 2024
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  2. plot.cca with optimize=T could over-write user parameters

    @jarioksa
    jarioksa committed Jul 29, 2024
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