Fixed an issue in foresttopr() where the first y-axis
label could be clipped or not displayed.
topr 2.0.3
Added the foresttopr() function.
Fixed a ggplot2 deprecation warning by replacing the
size aesthetic with linewidth.
Updated the default topr color palette accessed via
get_topr_colors().
The previous palette can still be retrieved using
get_topr_old_colors().
Added support for setting the base color in locuszoom plots.
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).