# topr 2.0.4
* 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).

# 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
