NEWS.md

In GenuityScience/topr: Create Custom Plots for Viewing Genetic Association Results

topr 2.0.2

• 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

• 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

• 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

• 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

• 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

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

topr 1.1.7

• 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

• Updated documentation

topr 1.1.5

• Fix for chrX when displaying genes in regionplot

topr 1.1.4

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

topr 1.1.3

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

topr 1.1.2

• 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

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

topr 1.1.0

• 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

• First official release of topr

topr 0.0.1

• First version including locuszoom plot

topr 0.0.0

• First version submitted to github

GenuityScience/topr documentation built on Oct. 20, 2024, 10:23 p.m.