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NEWS
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NEWS
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version 1.4.0
+ Release
CHANGES IN VERSION 1.2.1
------------------------
o Added EDLogo plots highlighting both enrichment and depletion
o Added new fill and border styles for the logos
o Added a Dirichlet Adaptive Shrinkage (dash) for adaptively scaling position weights
o Added tutorials in the vignette for multi panel Logos plots and combining Logolas plots with ggplot2 graphics.
o Some input arguments are deprecated or passed into control parameters
o Background matrix or vector option has been added for comparative logo plot visualization given a prior belief.
o PSSM logo plot function added primarily for protein sequence motif visualization
o Functions added to compute the heights of the enrichments and depletions of the symbols in logo plot.
o Nomenclature added for calling a base at each position.
CHANGES IN VERSION 1.2.1
------------------------
o Deprecated depletion weight input for unscaled logos + added unscaled log and
probKL and wKL approaches to the set of possible logos
CHANGES IN VERSION 1.4.0
------------------------
o deprecated the two functions - `logomaker` and `nlogomaker` for standard and EDLogo.
All logo plots can be now be generated using the same function - `logomaker()`. The
type argument in this function can be chosen to be Logo or EDLogo.
o trimmed the package down from nearly 60 exported functions to just 7 exported functions.
o The format of the input data is now made more flexible - it allows for a vector of character
sequences, along with the PFM or the PWM matrix as before (see vignette).
o changed the complicated `color_profile` argument into three separate arguments - a `color_type`
similar to `color_profile$type` argument before, a `colors` argument allowing user to choose a
cohort of colors, and a `color_seed` argument allowing the user to sample different colors from
the cohort. We now provide a default cohort of `colors` as well as default `color_type` in `per-row`
(see vignette). The user now can do with not worrying about defining `color_profile` at all, and use
the defaults instead and change the default cohort by `color_seed`.
(see vignette).
o added a `return_heights` option in `logomaker()` function that, when set to TRUE, returns the
information of the heights of the stacks used for both standard and EDLogo (see vignette).
o added a `use_dash` argument that, when set to TRUE, would automatically detect if the input is
a character sequence of PFM matrix and perform adaptive scaling of heights (see vignette).
o updated the vignette completely with major focus on the EDLogo representation and the use of the
current `logomaker()` functionality
o updated the README - with citation information and a demo example added.
o Updated the gallery codes (https://kkdey.github.io/Logolas-pages/Gallery.html) here to conform to the
new system of functions.
o Updated the HTML vignette (https://kkdey.github.io/Logolas-pages/workflow.html) to match with the pdf
version of the vignette attached with the package.
o updated README with examples from String logos (histones and mutation signatures).
o moved from having data under `inst/extdata` to the `data` folder.
o added a `demo` folder containing some test gallery examples.