# ggtreeExtra 1.19.1

+ supporting the ggplot2_v4. (2025-08-08, Fri)

# ggtreeExtra 1.18.0

+ Bioconductor 3.21 released, and Bioconductor 3.22 bump. (2025-04-17, Thu)

# ggtreeExtra 1.17.0

+ Bioconductor 3.20 released, and Bioconductor 3.21 version bump version. (2024-10-31, Thu)

# ggtreeExtra 1.15.0

+ Bioconductor 3.19 released, and Bioconductor 3.20 version bump version. (2024-05-14, Tue)

# ggtreeExtra 1.13.1

+ update rd.

# ggtreeExtra 1.13.0

+ 1.12.0 version released with Bioconductor 3.18 and 1.13.0 version was bumped with 
  Bioconductor 3.19 (devel) version. (2023-10-25, Wed)

# ggtreeExtra 1.10.0

+ 1.10.0 version released with Bioconductor 3.17, and 1.11.0 version was bumped
   with Bioconductor devel (3.18).  (2023-04-28, Fri)

# ggtreeExtra 1.9.2

+ add `limits` parameter in `axis.params` to display the range of x axis. (2023-03-08, Wed)
+ using `cli` to replace `warning` or `stop`. (2022-11-24, Thu)
+ using `rlang` to transfer the `geom` argument. (2022-11-24, Thu)
+ using `pwidth` to replace `width` when `x` only have one unique 
  value with `geom = geom_tile` and `width` is not provided. (2022-11-25, Fri)
  - <https://github.com/YuLab-SMU/ggtreeExtra/issues/11#issuecomment-873335702>
  - <https://github.com/YuLab-SMU/ggtreeExtra/issues/12>
  - <https://github.com/YuLab-SMU/ggtreeExtra/issues/25>
+ adding the `messages` to show how to adjust the `color` scale when the `color` 
  aesthetic was use internal with `geom=geom_boxplot` etc. (2022-12-01, Thu)
  - <https://github.com/YuLab-SMU/ggtree/issues/551>

# ggtreeExtra 1.9.1

+ import `cli` to avoid warning in checking, which is used by the latest `ggplot2` (2022-11-08, Tue)

# ggtreeExtra 1.8.0

+ Bioconductor RELEASE_3_16 (2022-11-04, Fri)

# ggtreeExtra 1.7.1 

+ fix a bug of subset data (when the `value` mapped to `x` aesthetic contains negative value.)
+ fix a bug when x of mapping in data is only one unique.
 - <https://github.com/YuLab-SMU/ggtreeExtra/issues/24>

# ggtreeExtra 1.6.0

+ Bioconductor 3.15 release and Bioconductor 3.16 (devel) version bump.

# ggtreeExtra 1.5.4

+ set `orientation` argument automatically, when it is not be provided and the `geom` has the parameter. (2022-03-24, Thu)

# ggtreeExtra 1.5.3

+ update the citation format. (2022-01-28, Fri)

# ggtreeExtra 1.5.2

+ import `geom_text` , which was used in the axis of `geom_fruit` with `do.call`. (2021-11-24, Wed)

# ggtreeExtra 1.5.1

+ update the lower limit of reference range in normalization precess. (2021-11-19, Fri)

# ggtreeExtra 1.4.0

+ Bioconductor 3.14 release.

# ggtreeExtra 1.3.6

+ fix the issue of `gridlines` when some data is removed. (2021-08-25, Wed)

# ggtreeExtra 1.3.5

+ update citation of `ggtreeExtra` (2021-08-25, Wed). 

# ggtreeExtra 1.3.4

+ fix the `compute_aes` to better compatible with `ggplot2` (>=3.3.4) (2021-08-09, Mon)
  - The `ggplot2` (>=3.3.4) introduced `computed_mapping`.

# ggtreeExtra 1.3.3

+ update reference. (2021-06-08, Tue)
+ fix vector logical check. (201-06-11, Fri)
  - c(TRUE, TRUE) && c(TRUE, TRUE) is not allowed in 
    devel environment of bioconductor 

# ggtreeExtra 1.3.1

+ `data` argument of `geom_fruit` support function input. (2021-05-20, Thu)
+ the argument of `axis.params` and `grid.params` can be assigned by intermediate variables. (2021-05-26, Wed)
  - <https://github.com/YuLab-SMU/ggtreeExtra/issues/9> 

# ggtreeExtra 1.3.0

+ new version release, and bump new devel version (1.3.0). (2021-05-20, Thu)

# ggtreeExtra 1.1.12

+ import `ggtree` to pass `BiocCheck`. (2021-05-14, Fri)

# ggtreeExtra 1.1.11

+ fix a bug to solve the problem (variable of x has `NA`). (2021-05-13, Thu)
  + <https://github.com/YuLab-SMU/ggtreeExtra/issues/8>

# ggtreeExtra 1.1.10

+ fix a bug for `compute_aes` ( This is 
  to support mapping aesthetics (x, not y in aes of geom_fruit) to functions of variables). (2021-05-10, Mon)

# ggtreeExtra 1.1.9

+ don't inherit `aes` (global aes from the `ggtree`). (2021-04-28, Wed)
+ `subset` in mapping also supports the data from `ggtree` object. (2021-04-29, Thu)
+ support mapping aesthetics (`x`, not `y` in `aes` of `geom_fruit`) to functions of variables. (2021-05-07, Fri)

# ggtreeExtra 1.1.8

+ add new `position` functions: `position_jitterx` and `position_jitterdodgex`. (2021-04-23, Fri)
+ update vignettes. (2021-04-25, Sun)

# ggtreeExtra 1.1.7

+ update man and vignettes. (2021-04-06, Tue)

# ggtreeExtra 1.1.6

+ check whether the value of x is numeric to avoid warnings when x is factor. (2021-02-24, Wed)
+ remove axis of first `geom_tile` of vignettes, since the axis of this layer is meaningless. (2021-02-24, wed)

# ggtreeExtra 1.1.5

+ support `title` of panel. (2021-02-03, Wed)
  - <https://github.com/YuLab-SMU/ggtreeExtra/issues/7>
+ add citation info. (2021-02-04, Thu)
+ don't use `svg` dev. (2021-02-04, Thu)

# ggtreeExtra 1.1.4

+ add `position_points_jitterx` and `position_raincloudx` for **geom** of `ggridges`. (2021-01-20, Wed)
+ supports `geom_msa` of `ggmsa`. (2021-01-21, Thu)
+ specific `position` method for specific *geom* method automatically. (2021-01-27, Wed)

# ggtreeExtra 1.1.3

+ support multiple density plot from **geom** of *ggridges*. (2020-12-31, Thu)
  `geom_density_ridges`, `geom_density_ridges2`, `geom_density_ridges_gradient`,
  `geom_ridgeline`, `geom_ridgeline_gradient`.

# ggtreeExtra 1.1.2

+ support `subset` in mapping, but the `data` should also be provided. (2020-11-30, Mon)
+ add default position methods for common geometric functions. (2020-12-18, Fri)

# ggtreeExtra 1.0.0

+ Bioconductor 3.12 release (2020-10-28, Wed)

## the 0.99.0 or 0.99.x version mean I am submitting it to `Bioconductor`. (20200710, Fri)

+ 0.99.1 change `svg` of `dev` to `png`, set the dpi to 300. (20200714, Tue)
+ 0.99.2 `geom_axis_text` support the single column axis. (20200717, Fri)
+ 0.99.3 support `inward_circular` tree and `geom_axis_text` was build by `position_identityx`. (20200724, Fri)
+ 0.99.4 fix the constant of `barplot` bug. (2020-07-25, Sat)
+ 0.99.5 better support the layer when x axis is reverse. (2020-07-29, Wed)
+ 0.99.6 support adjusting the angle of geom_text. (2020-07-31, Fri)
+ 0.99.7 revise stylistic comment of R code and examples. (2020-08-04, Tue)
+ 0.99.8 change the formatting of code chunk. (2020-08-04, Tue)
### 0.99.9
  + modified the `color` aesthetics for `geom_boxplot` and `geom_violin`. (2020-08-14, Fri)
  + keep all column of data of tree when it merge with external data. (2020-08-14, Fri)
### 0.99.10 
  + add `geom_ringline` to create the grid line of external ring layers. (2020-08-21, Fri)
  + the `addbrink` and other argument control the line of margin has been removed. (2020-08-21, Fri)
  + add pseudo axis line in `geom_axis_text`. (2020-08-21, Fri) 
### 0.99.11
  + `geom_axis_text` and `geom_ringline` are removed. (2020-08-24, Mon)
  + user can use `axis.params=list(add.axis=TRUE)` and `grid.params=list(add.grid=TRUE)` to
    add the axis and grid lines of external layers, respectively. (2020-08-24, Mon)
### 0.99.12
  + add upper and lower grid lines of y. (2020-08-26, Wed)
### 0.99.13
  + update the method of `ggplot_add.layer_fruits`, when the `offset` between different `fruit_plot` 
    is different, will use each `offset` in each `fruit_plot`. (2020-08-31, Mon)
### 0.99.14
  + update `normxy` to support `dendrogram` layout. (2020-09-02, Wed)
### 0.99.15
  + add `add.another.axis` in `geom_fruit` to add another axis. (2020-09-04, Fri)
  + update `normxy` to fix the bug when negative values are present. (2020-09-04, Fri)
  + update `ggplot_add` method of `geom_fruit` to support the orientation 
    which x axis of the external is from bottom to top, when layout is `dendrogram`. (2020-09-04, Fri)
### 0.99.16
  + change `add.axis` in axis.params from TRUE or FALSE to `x` or `y` or `xy`. (2020-09-05, Sat)
  + remove `add.grid` in `grid.params` and default of `grid.params` is NULL. (2020-09-07, Mon)
  + update method of `axis tick` and remove `nbreaks`, the breaks will be calculate by `pretty`. (2020-09-07, Mon)
  + use `substitute` to allow list of `axis.params` or `grid.params` has empty argument, 
    eg `grid.params=list(color="black",)`. (2020-09-07, Mon)
### 0.99.17
  + change `add.axis` to `axis` in `axis.params`. (2020-09-08, Tue)
### 0.99.18
  + add `nbreak` in `axis.params` of `geom_fruit`, it will be sent to `n` of `pretty` to 
    generate the desired number of intervals of `axis`. (2020-09-08, Tue)
### 0.99.19
  + modified the namespace, remove `geom_vline`, add `geom_segment`. (2020-09-11, Fri)
  
# 0.0.1

+ add vignettes. (20200707, Tue)

# 0.0.0.9

+ support add the axis text of extra layer of `geom_fruit` using `geom_axis_text`. (20200630, Tue)
+ optimize normalization of extra layer data. (20200701, Wed) 
+ fixed bug: changed layer to layers. (20200703, Fri)

# 0.0.0.8

+ support data of NULL in `geom_fruit`, and user can add data by `%<+%` of `ggtree`. (20200628, Sun)

# 0.0.0.7 

+ add `geom_fruit_list` to support add the same position for multi layers. (20200622, Mon)

# 0.0.0.6

+ automatically detect the 'position'. (20200612)

# 0.0.0.5

+ change `pratio` parameter to `pwidth` and remove `tippoint` parameter.
+ change `geom_add` function to `geom_totree` function. (20200610)

# 0.0.0.4

+ support tip point for `geom_star` or `geom_point`
+ support `geom_boxplot` and `geom_violin` (20200606)

# 0.0.0.3

+ add marginal line, and when x is character, the new x normalized 
  should be started with zero. (20200601)

# 0.0.0.2

+ The distance between the panel and tree can be adjusted 
  using the "offset". The value of associate panel were 
  normalized in the range of x of tree. The width can be 
  adjusted using the "pratio". The "offset" and "pratio" 
  are the ratio related to tree. (20200529)

# 0.0.0.1

+ first version to `github` (20200528)
