NEWS

ggtreeExtra 1.13.0

Bioconductor 3.18 released and Bioconductor 3.19 (devel) version bump. (2023-10-25, Wed)

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)
- 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)

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)