NEWS
ggtreeExtra 1.23.1
- introduce
text.height in axis.params parameter in geom_fruit. (2026-06-04, Thu)
ggtreeExtra 1.23.0
- Bioconductor 3.23 released, and Bioconductor 3.24 (devel) bump. (2025-04-29, Wed)
ggtreeExtra 1.21.0
- Bioconductor 3.22 released, and Bioconductor 3.23 (devel) bump. (2025-10-31, Fri)
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
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)
- 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)
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.
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)
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)
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)
- 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)
ggtreeExtra 0.0.1
- add vignettes. (20200707, Tue)
ggtreeExtra 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)
ggtreeExtra 0.0.0.8
- support data of NULL in
geom_fruit, and user can add data by %<+% of ggtree. (20200628, Sun)
ggtreeExtra 0.0.0.7
- add
geom_fruit_list to support add the same position for multi layers. (20200622, Mon)
ggtreeExtra 0.0.0.6
- automatically detect the 'position'. (20200612)
ggtreeExtra 0.0.0.5
- change
pratio parameter to pwidth and remove tippoint parameter.
- change
geom_add function to geom_totree function. (20200610)
ggtreeExtra 0.0.0.4
- support tip point for
geom_star or geom_point
- support
geom_boxplot and geom_violin (20200606)
ggtreeExtra 0.0.0.3
- add marginal line, and when x is character, the new x normalized
should be started with zero. (20200601)
ggtreeExtra 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)
ggtreeExtra 0.0.0.1
- first version to
github (20200528)