Changes in version 1.13.0
- Bioconductor 3.18 released and Bioconductor 3.19 (devel) version
bump. (2023-10-25, Wed)
Changes in version 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
Changes in version 1.9.1
- import cli to avoid warning in checking, which is used by the latest
ggplot2 (2022-11-08, Tue)
Changes in version 1.8.0
- Bioconductor RELEASE_3_16 (2022-11-04, Fri)
Changes in version 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
Changes in version 1.6.0
- Bioconductor 3.15 release and Bioconductor 3.16 (devel) version
bump.
Changes in version 1.5.4
- set orientation argument automatically, when it is not be provided
and the geom has the parameter. (2022-03-24, Thu)
Changes in version 1.5.3
- update the citation format. (2022-01-28, Fri)
Changes in version 1.5.2
- import geom_text , which was used in the axis of geom_fruit with
do.call. (2021-11-24, Wed)
Changes in version 1.5.1
- update the lower limit of reference range in normalization precess.
(2021-11-19, Fri)
Changes in version 1.4.0
- Bioconductor 3.14 release.
Changes in version 1.3.6
- fix the issue of gridlines when some data is removed. (2021-08-25,
Wed)
Changes in version 1.3.5
- update citation of ggtreeExtra (2021-08-25, Wed).
Changes in version 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.
Changes in version 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
Changes in version 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
Changes in version 1.3.0
- new version release, and bump new devel version (1.3.0).
(2021-05-20, Thu)
Changes in version 1.1.12
- import ggtree to pass BiocCheck. (2021-05-14, Fri)
Changes in version 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
Changes in version 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)
Changes in version 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)
Changes in version 1.1.8
- add new position functions: position_jitterx and
position_jitterdodgex. (2021-04-23, Fri)
- update vignettes. (2021-04-25, Sun)
Changes in version 1.1.7
- update man and vignettes. (2021-04-06, Tue)
Changes in version 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)
Changes in version 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)
Changes in version 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)
Changes in version 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.
Changes in version 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)
Changes in version 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)
Changes in version 0.0.1
- add vignettes. (20200707, Tue)
Changes in version 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)
Changes in version 0.0.0.8
- support data of NULL in geom_fruit, and user can add data by %<+% of
ggtree. (20200628, Sun)
Changes in version 0.0.0.7
- add geom_fruit_list to support add the same position for multi
layers. (20200622, Mon)
Changes in version 0.0.0.6
- automatically detect the 'position'. (20200612)
Changes in version 0.0.0.5
- change pratio parameter to pwidth and remove tippoint parameter.
- change geom_add function to geom_totree function. (20200610)
Changes in version 0.0.0.4
- support tip point for geom_star or geom_point
- support geom_boxplot and geom_violin (20200606)
Changes in version 0.0.0.3
- add marginal line, and when x is character, the new x normalized
should be started with zero. (20200601)
Changes in version 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)
Changes in version 0.0.0.1
- first version to github (20200528)