NEWS.md

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

MicrobiotaProcess 1.19.0

• Bioconductor 3.20 release, and Biocondutor 3.21 (devel) version bump. (2024-10-31, Thu)

MicrobiotaProcess 1.17.1

• update scale_fill_diff_cladogram to be compatible with ggnewscale >= 0.5.0 (2024-07-24, Wed)

MicrobiotaProcess 1.17.0

• Bioconductor 3.19 release, and Biocondutor 3.20 (devel) version bump. (2024-05-14, Tue)

MicrobiotaProcess 1.15.1

• fix a bug of mp_import_qiime when sample metadata has - character. (2024-04-12, Fri)
• update mp_plot_diff_cladogram with tidytree and treeio. (2024-03-26, Tue)

MicrobiotaProcess 1.15.0

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

MicrobiotaProcess 1.13.3

• fix the issue when assays is dgCMatrix other sparse matrix class. (2023-09-12, Tue)
• using internal functions to convert dist object to tbl_df or tbl_df to dist in mp_cal_dist and fix a bug of mp_extract_abundance when rowData contains list metadata information. (2023-08-21, Mon)
• update the doc of rmun argument in mp_plot_abundance to avoid misunderstanding. (2023-08-18, Fri) https://github.com/YuLab-SMU/MicrobiotaProcess/issues/99
• update mp_import_humann_regroup() to keep the abundance of contributed taxa in each sample with keep.contribute.abundance=TRUE. (2023-08-15, Tue)
• use rlang::check_installed() to check if a suggested package is installed, which will offer to install the package before continuing. (2023-08-02, Wed)
• introduce order.by.feature argument in mp_plot_abundance to adjust the sample order. (2023-07-24, Mon)
• update the format of citation and suppress the message introduced by tidytree. (2023-07-14, Fri)

MicrobiotaProcess 1.13.2

• update mp_plot_ord to display the result of mp_adonis with show.adonis = TRUE. (2023-06-21, Wed)
• using theme_blinds of ggfun. (2023-06-20, Tue)
• add mp_import_humann_regroup function to parsing the output of humann_regroup_table. (2023-05-15, Mon)
• add fortify method for MPSE object. (2023-05-18, Thu)
• fix a bug of mp_plot_diff_res when ggnewscale updated to 0.4.9. (2023-05-30, Tue)

MicrobiotaProcess 1.13.1

• fix a bug for the abundance calculation with force = TRUE and relative = FALSE. (2023-04-28, Fri)

MicrobiotaProcess 1.11.5

• update ggdiffclade using the geom layer of ggtree. (2023-03-02)
• update mp_cal_dist to support storing the distance between the features with action='add'. (2023-03-28)
• fix the special symbol in group name with mp_diff_analysis. (2023-04-11)

MicrobiotaProcess 1.11.4

• update mp_plot_diff_res and mp_plot_diff_boxplot to support visualize the abundance (not relative abundance). (2022-12-02, Fri)
• fix the tip.label and rownames of assays when tree is provided in mp_import_dada2 (2022-12-02, Fri)
• add the message information when the differential features was filtered in the first and second test in mp_diff_analysis. (2022-12-06, Tue)
• fix the dynamic dots issue of left_join. (2022-12-15, Thu)

MicrobiotaProcess 1.11.3

• update mp_plot_abundance to be compatible with the latest ggplot2. (2022-11-08, Tue)
• add mp_plot_diff_manhattan to visualize the different results with manhattan plot. (2022-11-21, Mon)

MicrobiotaProcess 1.9.5

• fix the color of mp_plot_diff_boxplot and update mp_plot_abundance. (2022-10-27, Thu)

MicrobiotaProcess 1.9.4

• keep the consistent color between the panels of mp_plot_diff_boxplot. (2022-10-18, Tue)
• optimizing the import of dtplyr. (2022-10-14, Fri)
• update mp_plot_diff_res to support the custom DAA results. (2022-09-27, Tue)
• update show method of MPSE to avoid the colname advice. (2022-09-27, Tue)
• add mp_dmn, mp_dmngroup, mp_divergence and update mp_plot_diff_boxplot, mp_plot_diff_cladogram to support the custom style. (2022-09-25, Sun)
• update mp_cal_dist to support specifying distmethod to a function. (2022-09-20, Tue)
• update left_join to support joining the dist class. (2022-09-20, Tue)

MicrobiotaProcess 1.9.3

• fix a bug of mp_plot_diff_boxplot when taxatree slot is NULL. (2022-08-22, Mon)

MicrobiotaProcess 1.9.2

• fixed the local vignettes. (2022-07-06, Wed)
• add mp_import_biom to build MPSE class from biom-format file. (2022-07-13, Wed)
• add 'mp_plot_diff_boxplot' to replace ggdiffbox. (2022-07-29, Fri)

MicrobiotaProcess 1.9.1

• fix the color of legend in mp_plot_diff_cladogram. (2022-05-25)
• add mp_plot_diff_cladogram in vignetters. (2022-05-14)
• fixed a bug when the total counts of sample is less than chunks in mp_plot_rarecurve. (2022-05-14)
• add rm.zero argument in mp_plot_abundance to control whether mask the zero abundance of species. (2022-05-06)
• add taxa.class argument in mp_diff_analysis to test the specified taxa level. (2022-04-28)

MicrobiotaProcess 1.8.0

• Bioconductor 3.15 release. (2022-04-27)

MicrobiotaProcess 1.7.11

• add mp_plot_diff_cladogram to plot the result of mp_diff_analysis. (2022-04-19)

MicrobiotaProcess 1.7.10

• optimizing the mp_aggregate_clade and mp_balance_clade. (2022-04-13)

MicrobiotaProcess 1.7.9

• add mp_cal_pd_metric to calculate the related phylogenetic diversity metrics. (2022-04-02) including NRI, NTI, PD, PAE, HAED, EAED, IAC.
• add mp_balance_clade to calculate the balance score of internal nodes according to their tip nodes abundances. (2022-03-22)
• add extract_binary_offspring to find the descendant tip/internal/all (with type parameter) nodes. (2022-03-17)
• add mp_aggregate_clade and mp_diff_clade to calculate and test the abundance (differential signals) of internal node according to their tip nodes abundance. (2022-03-16)
• add mp_select_as_tip and fix the bug of mp_diff_analysis with specific tip.level (not OTU) argument. (2022-03-02, Mon)
• fix the replace_na bug of new tidyr. (2022-03-04, Fri)
• update mp_import_metaphlan to better parse the output of MetaPhlAn2. (2022-03-11, Fri)
• update the mp_cal_abundance to return the tbl_df contained numeric type sample metadata. (2022-03-11, Fri)

MicrobiotaProcess 1.7.8

• supporting multiple group names and supporting numeric type for .group of mp_plot_alpha. (2022-02-15, Tue)
• supporting multiple group names for .group of mp_plot_abundance when plot.group=TRUE. (2022-02-14, Mon)
• fix the width of mp_plot_abundance with geom="flowbar". (2022-02-01, Tue)
• related issue

MicrobiotaProcess 1.7.7

• fix the bug about the constant variables within groups in lda of MASS (2022-01-27, Thu)

MicrobiotaProcess 1.7.6

• fix the issue, that kingdom level of taxonomy information contains k__ or K__, which is unknown annotation in kingdom. (2021-01-14, Fri)
• add mp_extract_taxatree and mp_extract_otutree (alias of mp_extract_tree). (2022-01-14, Fri)

MicrobiotaProcess 1.7.5

• add the message for the not integers in mp_cal_alpha. (2021-12-31, Fri)
• remove the features which variance of their abundance is zero before identify different taxa. (2021-12-28, Tue)
• add bar option in mp_plot_abundance, default is flowbar, the other options are bar and heatmap
• use corrected relative eigenvalues when the eigenvalues has negative values. (2021-12-27, Mon)
• add new distmethod from hopach. (2021-12-27, Mon)
• update tax_table without required phyloseq. (2021-12-20, Mon)
• update mp_diff_analysis to support the factor type group (.group specified). (2021-12-20, Mon)

MicrobiotaProcess 1.7.4

• update taxatree<- and otutree<- which will extract the intersection between the tip labels of input treedata and the rownames of MPSE. (2021-12-14, Tue)
• add taxonomy<- for MPSE to assign the taxonomy information, which will be converted to taxatree automatically. (2021-12-14, Tue)
• add tax_table for MPSE and return taxonomyTable defined in phyloseq. (2021-12-14, Tue)
• update mp_import_metaphlan to better parse the output of MetaPhlAn2. (2021-11-30, Tue)

MicrobiotaProcess 1.7.3

• update 'mp_plot_abundance' (2021-11-24, Wed)
• support heatmap by setting geom.
• .group supports multiple characters and .sec.group will be removed in the next version.
• update mp_plot_diff_res (2021-11-23, Tue)
• support otutree and taxatree class by setting tree.type.
• support multiple layout types of tree by setting layout.
• support adjusting the gap between panel and width of panel by setting offset.abun, pwidth.abun, offset.effsize, pwidth.effsize
• support whether display the relative abundance of group instead of sample by setting group.abun=TRUE or sample number > 50
• add mp_plot_diff_res to visualize the result of mp_diff_analysis. (2021-11-22, Mon)

MicrobiotaProcess 1.7.2

• speed up the mp_cal_abundance, mp_cal_venn and mp_cal_upset with dtplyr. (2021-11-18, Thu)
• update the guide of x axis of ggside in mp_plot_ord. (2021-11-15, Mon)
• update mp_plot_abundance to visualize the abundance of taxonomy from high (bottom) to low (top). (2021-11-15, Mon)
• support multiple annotation rows or cols of heatmap of mp_plot_dist with .group=c(group1, group2), and add set_scale_theme to adjust the scale or theme of subplot of heatmap. (2021-11-10, Wed)
• fix the issue when the taxonomy info is removed with select. (2021-11-09, Tue)
• update print for MPSE class. (2021-11-09, Tue)
• update otutree<- for support phylo class. (2021-11-09, Tue)
• speed up the integration of mp_cal_dist result with action="add". (2021-11-09, Tue)
• update as.MPSE for biom class to support parsing the metadata of sample. (2021-11-09, Tue)

MicrobiotaProcess 1.7.1

• fix the issue when using filter only return a assays contained one feature (nrow=1). (2021-11-05, Fri)
• fix the error of rownames<- when rownames of MPSE is NULL. (2021-11-04, Thu)
• update 'message' or 'stop error message' when the 'Abundance' cannot be rarefied in some functions, such as mp_cal_alpha, mp_cal_venn, mp_cal_upset, mp_cal_abundance and mp_cal_NRT_NTI. (2021-10-29, Fri)
• introduce .sec.group argument to specify the second group name in mp_plot_abundance, if it is provided, the nested facet will be displayed. (2021-11-02, Tue)

MicrobiotaProcess 1.6.0

• Bioconductor 3.14 release. (2021-10-27, Wed)

MicrobiotaProcess 1.5.9

• add include.rownames to control whether consider the OTU as taxonomy feature table in diff_analysis and get_alltaxadf or tip labels in as.treedata. (2021-10-19, Tue)
• fix rename bug, rename the taxonomy names can work now. (2021-10-12, Tue)
• introduce trimSample in mp_rrarefy to check whether to remove the samples that do not have enough abundance. (2021-10-11, Mon)
• update MPSE to allow assays supporting data.frame or DFrame class. (2021-10-08, Fri)
• update mp_plot_ord to suppress the message of the third depend package. (2021-10-08, Fri)

MicrobiotaProcess 1.5.8

• 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)

MicrobiotaProcess 1.5.7

• fix bug of mp_plot_upset. (2021-09-10, Fri)
• update the mp_plot_ord. (2021-09-13, Mon)

MicrobiotaProcess 1.5.6

• 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)

MicrobiotaProcess 1.5.5

• 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)

MicrobiotaProcess 1.5.4

• 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)

MicrobiotaProcess 1.5.3

• 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)

MicrobiotaProcess 1.5.2

• 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

MicrobiotaProcess 1.5.1

• 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)

MicrobiotaProcess 1.4.0

• new version released. (2021-05-20, Thu)

MicrobiotaProcess 1.3.11

• fill ggclust bug to map color and shape. (2021-05-12, Wed)

MicrobiotaProcess 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

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

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.