NEWS.md

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

MicrobiotaProcess 1.3.8

• rename files of code. (2021-03-23, Tue)
• add aliases for ggbartaxa and ggdiffbartaxa. (2021-03-23, Tue)

MicrobiotaProcess 1.3.7

• optimized import for installation. (2021-03-15, Mon)
• add sampleLevels in ggbartax to adjust the order of axis label. (2021-03-12, Fri)
• update import_qiime2 to avoid error when only feature table is provided. (2021-02-26, Fri)

MicrobiotaProcess 1.3.6

• convert svg dev to pdf dev. (2021-02-04, Thu)

MicrobiotaProcess 1.3.5

• fix an error for example of ggrarecurve. (2021-01-07, Thu) factorNames="Group" to factorNames="group"

MicrobiotaProcess 1.3.4

• fix a bug for numeric sample name. (2020-11-26, Thu)
• geom_tiplab also support circular layout, so remove geom_tiplab2. (2020-11-26, Thu)

MicrobiotaProcess 1.3.3

• add as.treedata for taxonomyTable class. (2020-11-23, Mon)

MicrobiotaProcess 1.3.2

• ggrarecurve can be set color with variable of group for each samples. (2020-11-11, Tue)
• using shadow=FALSE and providing factorNames
• https://github.com/YuLab-SMU/MicrobiotaProcess/issues/21
• add get_rarecurve to avoid repeated calculation when displaying rare curve. (2020-11-17, Tue)
• rareres <- get_rarecurve(obj, chunks=400) p <- ggrarecurve(rareres)

MicrobiotaProcess 1.3.1

• ggordpoint add showsample to show the labels of sample. (2020-10-29, Thu)
• the point of ggordpoint use the points of ggstar. (2020-10-30, Fri)
• to obtain the dynamic arguments of diff_analysis, the call was changed to someparams. someparams contained the arguments used in other functions. (2020-11-09, Mon)
• https://github.com/YuLab-SMU/MicrobiotaProcess/issues/20

MicrobiotaProcess 1.2.0

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

MicrobiotaProcess 1.1.13

• removed retrieve_seq and mapply_retrieve_seq function, since these need internet. Which might cause time out when check. (2020-10-16, Fri)

MicrobiotaProcess 1.1.12

• modified a bug in diff_analysis.phyloseq: change tax_table(ps) to ps@tax_table to avoid generate error when tax_table is NULL. (2020-10-15, Thu)

MicrobiotaProcess 1.1.11

• update the examples of drop_taxa. (2020-10-14, Wed)

MicrobiotaProcess 1.1.10

• update ggdiffclade to support data.frame input when reduce is TRUE. (2020-08-28, Fri)

MicrobiotaProcess 1.1.9

• update ggordpoint to fit the usage when user want to set mapping by manually. (2020-08-25, Tue)

MicrobiotaProcess 1.1.8

• get_taxadf, get_alltaxadf and diff_analysis has supported function datasets or other type datasets. (2020-08-17, Mon)

MicrobiotaProcess 1.1.7

• bugfix: cladetext argument has been omitted in ggdiffclade, now it has been fixed. (2020-08-14, Fri)
• deprecated argument: the size argument controlled the width of line of tree has been deprecated. The linewd replace it (2020-08-14, Fri).

MicrobiotaProcess 1.1.6

• removeUnkown argument has been replaced with removeUnknown in ggdiffbox, ggeffectsize, ggdifftaxbar and ggdiffclade. (2020-08-12, Wed)
• class argument has been replaced with classgroup in diff_analysis. (2020-08-12, Wed)
• add inward_circular layout in ggdiffclade. (2020-08-12, Wed)

MicrobiotaProcess 1.1.5

• ggdifftaxbar supports png, tiff format. (2020-08-10, Mon)
• add stop information to state the class argument in diff_analysis. (2020-08-10, Mon)

MicrobiotaProcess 1.1.4

• add tax_table information to result of get_taxadf. (2020-08-07, Fri)

MicrobiotaProcess 1.1.3

• change according to dplyr (v=1.0.0) (2020-08-05, Wed)
• remove rename_ and group_by_
• modified the angle to 90 in ggdiffclade when layout is slanted or rectangular (2020-08-05, Wed)

MicrobiotaProcess 1.1.2

• fix a bug. When the first rank taxa level (Kingdom) is NA.

Changes in version 0.99.1 (2020-03-03)

• First release of Bioconductor

Changes in version 0.99.0 (2019-08-14)

• Submitted to Bioconductor

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.