NEWS.md

In YuLab-SMU/ggtreeExtra: An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

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)

YuLab-SMU/ggtreeExtra documentation built on May 15, 2024, 10:02 p.m.