Changes in version 1.4.4 - fix the bug of AsIs list class in unnest for the tidyr (>= 1.1.4). (2021-10-01, Fri) - add mp_aggregate function. (2021-09-26, Sun) Changes in version 1.4.3 - fix issues of vignettes. (2021-09-18, Sat) - fix bug of mp_plot_upset. (2021-09-10, Fri) - update the mp_plot_ord. (2021-09-13, Mon) - convert the type of first element of assays to matrix to compatible with DESeqDataSet of DESeq2, test_differential_abundance of tidybulk. (2021-09-09, Thu) - update show and print for format output of MPSE class. (2021-09-08, Wed) - update mp_cal_abundance use new tidytree. (2021-09-07, Tue) - introduce include.lowest parameter in mp_filter_taxa. (2021-09-07, Tue) - update mp_plot_ord to display the bioplot for result of cca, rda and envfit. (2021-09-06, Mon) - update the vignettes of MicrobiotaProcess. (2021-09-04, Sat) - return updated MPSE object after the mp_diff_analysis is done with action="add". (2021-08-31, Fri) - then the taxtree and otutree with the result of different analysis can be extracted with mp_extract_tree. - fix issue print for one line of MPSE and update mp_plot_ord to display the side boxplot. (2021-08-31, Tue) - add mp_plot_ord for MPSE or tbl_mpse object after one of mp_cal_pca, mp_cal_pcoa, mp_cal_rda, mp_cal_nmds, mp_cal_rda, mp_cal_cca, mp_cal_dca or mp_envfit has been run with action='add'. (2021-08-30, Mon) - add mp_plot_dist for MPSE or tbl_mpse object after mp_cal_dist is performed with action="add". (2021-08-28, Sat) - add mp_plot_abundance, mp_plot_alpha, mp_plot_rarecurve, mp_plot_venn, mp_plot_upset for MPSE after the corresponding mp_cal_abundance, mp_cal_alpha, mp_cal_rarecurve, mp_cal_venn, mp_cal_upset are performed with action="add". (2021-08-27, Fri) - fix the issue when the rowname or colnames of SummarizedExperiment is NULL for as.MPSE. (2021-08-26, Thu) - fix the rownames of assays and colnames of colData to identical for SummarizedExperiment(1.23.3). (2021-08-26, Thu) - add mp_extract_refseq for MPSE object. (2021-08-25, Wed) - update as.MPSE for SummarizedExperiment object. (2021-08-24, Tue) - add mp_filter_taxa to drop the taxa that low abundance and low occurrences. (2021-08-24, Tue) - add colData<- and left_join for MPSE. (2021-08-23, Mon) - fix mutate for MPSE object. - don't import the parse_taxonomy_greengenes and parse_taxonomy_qiime from phyloseq. (2021-08-17, Tue) - add as.MPSE for TreeSummarizedExperiment class. (2021-08-17, Tue) - add mp_import_metaphlan to parsing the output of MetaPhlAn. (2021-08-12, Thu) - add treefile argument to import the tree of MetaPhlAn3 (mpa_v30_CHOCOPhlAn_201901_species_tree.nwk) (2021-08-13, Fri) - update the print of MPSE object via pillar package. (2021-08-06, Fri) - update mp_extract_dist by introducing .group argument to return a tbl_df for visualization. (2021-08-04, Wed) - add taxatree, taxatree<-, otutree, otutree<-, refseq, refseq<- for MPSE. (2021-08-04, Wed) - add mp_extract_rarecurve to extract the result of mp_cal_rarecurve from MPSE or tbl_mpse object. (2021-08-04, Wed) - add mp_stat_taxa to count the number and total number taxa for each sample at different taxonomy levels (Kingdom, Phylum, Class, Order, Family, Genus, Species, OTU). (2021-08-03, Tue) - rename mp_extract_abundance to mp_extract_assays from MPSE or tbl_mpse. (2021-07-31, Sat) - update the method to save the result of mp_cal_clust by introducing action argument. (2021-07-29, Thu). - update as.phyloseq for MPSE or tbl_mpse object. (2021-07-28, Wed) - add mp_diff_analysis for MPSE or tbl_mpse object. (2021-07-27, Tue) - add dr_extract for the visualization of the result of ordination. (2021-07-26, Mon) - comment out the function for phyloseq and add rd of the function for MPSE or tbl_mpse. (2021-07-24, Sat) - update the function to parsing the result of rda, cca, envfit. (2021-07-23, Fri) - add tidydr to convert the result of reduce dimension to tbl_df - such pca, pcoa, nmds, rda, cca. (2021-07-22, Thu) - optimize the print for MPSE. (2021-07-22, Thu) - add mp_mantel and mp_mrpp for MPSE or tbl_mpse object. (2021-07-19, Mon) - add mp_envfit and update mp_cal_dist to support the distance calculation with continuous environment factors and rename mp_cal_adonis to mp_adonis, mp_cal_anosim to mp_anosim. (2021-07-17, Sat) - add mp_cal_rda, mp_cal_cca, mp_cal_adonis and mp_cal_anosim for MPSE or tbl_mpse object. (2021-07-16, Fri) - add mp_cal_dca, mp_cal_nmds and mp_extract_internal_attr. (2021-07-15, Thu) - add mp_cal_pca, mp_cal_pcoa and mp_extract_abundance. (2021-07-14, Wed) - add mp_cal_clust to perform the hierarchical cluster analysis of samples and mp_extract_dist to extract the dist object from MPSE object or tbl_mpse object. (2021-07-13, Thu) - add mp_cal_dist to calculate the distance between samples with MPSE or tbl_mpse object. (2021-07-12, Mon) - add mp_extract_sample, mp_extract_taxonomy, mp_extract_feature to extract the sample, taxonomy and feature (OTU) information and return tbl_df or data.frame. (2021-07-09, Fri) - add mp_cal_venn to build the input for venn plot (2021-07-09, Fri) - mp_cal_rarecurve add action argument to control whether the result will be added to MPSE and tbl_mpse or return directly. (2021-07-08, Thu) - add mp_cal_upset to get the input of ggupset. (2021-07-08, Thu) - add mp_extract_tree to extract the otutree or taxatree from MPSE or tbl_mpse object. (2021-07-07, Wed) - add pull and slice to support the MPSE object. (2021-07-06, Tue) - add mp_cal_rarecurve to calculate the rarecurve of each sample with MPSE or tbl_mpse. (2021-07-06, Tue) - add mp_cal_abundance to calculate the relative abundance of each taxonomy class with MPSE or tbl_mpse. (2021-07-05, Mon) - add mp_decostand provided several standardization methods for MPSE, tbl_mpse and grouped_df_mpse. (2021-07-04, Sun) - add mp_import_qiime to parse the output of qiime old version. (2021-07-03, Sat) - add taxatree slot to MPSE. (2021-06-30, Wed) - add mp_cal_alpha function for MPSE or mpse object. (2021-07-01, Thu) - add rownames<- to support renaming the names of feature. (2021-07-01, Thu) - add mp_import_qiime2 and mp_import_dada2 to parse the output of dada2 or qiime2 and return MPSE object. (2021-07-02, Fri) - update print information for MPSE, tbl_mpse and grouped_df_mpse. (2021-06-29, Tue) - add [ to the accessors of MPSE. (2021-06-29, Tue) - use MPSE object. (2021-06-28, Mon) - add as.MPSE to convert phyloseq or tbl_mpse to MPSE class. - Formatted output. - tidy framework for MPSE object. - as_tibble to convert MPSE and phyloseq to tbl_mpse. (2021-06-28, Mon) - filter to subset a data frame from tbl_mpse. (2021-06-28, Mon) - group_by to do some data operations on groups for tbl_mpse. (2021-06-28, Mon) - arrange to order the rows of a data frame for tbl_mpse. (2021-06-28, Mon) - mutate to adds new variables and preserves existing ones for tbl_mpse. (2021-06-28, Mon) - select to select variables in tbl_mpse. (2021-06-28, Mon) - distinct to select only unique/distinct rows in tbl_mpse. (2021-06-28, Mon) - rename to rename the variable names in tbl_mpse. (2021-06-28, Mon) - nest to create a list-column of tbl_mpse, it will convert tbl_mpse to tbl_mpse_nest. (2021-06-28, Mon) - unnest to convert the tbl_mpse_nest to tbl_mpse. (2021-06-28, Mon) - as.treedata to convert tbl_mpse to treedata, then we can explore the data with treedata. - add tiplevel argument to control whether use OTU as tip label, default is OTU. (2021-06-28, Mon) - left_join to mutate joins based the left tbl_mpse structure. (2021-06-28, Mon) - changed clustplotClass to treedata. (2021-06-28, Tue) - add mp_rrarefy method to rarefy species richness. (2021-06-29, Tue) - it supports MPSE, tbl_mpse, grouped_df_mpse object via wrapping vegan::rrarefy. - ~~update as.MPSE and as.treedata for grouped_df_mpse object. (2021-06-29, Tue)~~ ~~- This feature is useful to explore the microbiome data in taxa tree.~~ This feature has been replaced by the taxatree slot - add ellipse_linewd and ellipse_lty in ggordpoint to control the width and line type of ellipse line. (2021-05-24, Mon) - fixed the regular expression match for the internal function to print the results of diff_analysis. (2021-06-06, Sun) - add filter function to filter the result of diff_analysis. (2021-06-07, Mon) - more accessor function for result of diff_analysis. (2021-06-07, Mon) - head - tail - [ - [[]] - $ - dim - add get_NRI_NTI to calculate the NRI and NTI. (2021-06-08, Tue) Changes in version 1.4.0 - new version released. (2021-05-20, Thu) Changes in version 1.3.11 - fill ggclust bug to map color and shape. (2021-05-12, Wed) Changes in version 1.3.9 - more layouts for ggdiffclade. (2021-04-16, Fri) - remove unclassified, ambiguous taxonomy names. (2021-03-30, Tue) - https://github.com/YuLab-SMU/MicrobiotaProcess/issues/23 Changes in version 1.3.8 - rename files of code. (2021-03-23, Tue) - add aliases for ggbartaxa and ggdiffbartaxa. (2021-03-23, Tue) Changes in version 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) Changes in version 1.3.6 - convert svg dev to pdf dev. (2021-02-04, Thu) Changes in version 1.3.5 - fix an error for example of ggrarecurve. (2021-01-07, Thu) factorNames="Group" to factorNames="group" Changes in version 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) Changes in version 1.3.3 - add as.treedata for taxonomyTable class. (2020-11-23, Mon) Changes in version 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) Changes in version 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 Changes in version 1.2.0 - Bioconductor 3.12 release (2020-10-28, Wed) Changes in version 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) Changes in version 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) Changes in version 1.1.11 - update the examples of drop_taxa. (2020-10-14, Wed) Changes in version 1.1.10 - update ggdiffclade to support data.frame input when reduce is TRUE. (2020-08-28, Fri) Changes in version 1.1.9 - update ggordpoint to fit the usage when user want to set mapping by manually. (2020-08-25, Tue) Changes in version 1.1.8 - get_taxadf, get_alltaxadf and diff_analysis has supported function datasets or other type datasets. (2020-08-17, Mon) Changes in version 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). Changes in version 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) Changes in version 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) Changes in version 1.1.4 - add tax_table information to result of get_taxadf. (2020-08-07, Fri) Changes in version 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) Changes in version 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