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Changelog

Source: NEWS.md

topr 2.0.2

CRAN release: 2024-06-19

  • Parameters added for downsampling/thinning the dataset prior to plotting with manhattan
  • Locuszoom plot updated to include variants with missing R2 values
  • vline_color bug fix
  • Improved get_lead_snp functionality
  • The get_sign_and_sugg_loci function added for extracting genome-wide significant and suggestive loci
  • The manhattanExtra function added for highlighting genome-wide significant and suggestive loci

topr 2.0.1

CRAN release: 2024-03-15

  • REF and ALT error message fixed when there are p-values below .Machine$double.xmin in the input dataset
  • The limits= argument added in the scale_color_manual ggplot2 function for it to work as expected with ggplot2 v3.5

topr 2.0.0

CRAN release: 2024-02-04

  • topr can now be used with any species
  • argument added to set the color of the diagonal line in qqtopr
  • Argument chr_ticknames, show_all_chrticks, hide_chrticks_from_pos, hide_chrticks_to_pos and hide_every_nth_chrtick added to the Manhattan function to control x-axis labels
  • The log_trans_p argument was added for input datasets that have already been log-transformed
  • Inclusion of chromosomes Y and MT in build hg38

topr 1.1.10

CRAN release: 2023-09-13

  • Argument get_chr_lengths_from_data added to the Manhattan function so the number of chromosomes and chromosome lengths can be extracted from the input data.
  • The Manhattan plot displays as many chromosomes as are in the input data.

topr 1.1.9

CRAN release: 2023-09-06

  • Correct gene annotation used in regionplot when using build 37
  • Fix of partly incorrect coloring of association points near the end or beginning of a chromosome.

topr 1.1.8

CRAN release: 2023-08-26

  • Missing shade added for chr22 on Manhattan plot when chrX is not included in the dataset.

topr 1.1.7

CRAN release: 2023-05-23

  • Placeholder added when there are no genes in the region on display
  • Fix for the manhattan function to handle one chromosome datasets
  • xaxis_label added as an input argument to the manhattan plot function

topr 1.1.6

CRAN release: 2023-04-26

  • Updated documentation

topr 1.1.5

CRAN release: 2023-04-25

  • Fix for chrX when displaying genes in regionplot

topr 1.1.4

CRAN release: 2023-03-09

  • Default significance threshold changed from 5e-9 to 5e-8
  • Updated README

topr 1.1.3

CRAN release: 2023-02-12

  • Fix to make topr compatible with the next version of dplyr

topr 1.1.2

CRAN release: 2023-01-13

  • the scale parameter for annotate_with_vline was fixed
  • the Manhattan plot was changed to the more conventional two-color display
  • the argument theme_grey can be set to TRUE to make the Manhattan plot look like it does in older versions of topr

topr 1.1.1

CRAN release: 2022-11-04

  • Minor bug fix for plot colors and legends when plotting multiple datasets
  • region argument added to the manhattan function

topr 1.1.0

CRAN release: 2022-10-25

  • Update to increase control over plot aesthetics and variant labeling
  • minor bug fixes
  • Includes the option to choose between genome builds 38 (GRCh38.p13) and 37 (GRCh37.p13).

topr 1.0.0

CRAN release: 2022-01-12

  • First official release of topr

topr 0.0.1

  • First version including locuszoom plot

topr 0.0.0

  • First version submitted to github