scale_fill_diff_cladogram to be compatible with ggnewscale >= 0.5.0 (2024-07-24, Wed)mp_import_qiime when sample metadata has - character. (2024-04-12, Fri)mp_plot_diff_cladogram with tidytree and treeio. (2024-03-26, Tue)assays is dgCMatrix other sparse matrix class. (2023-09-12, Tue)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)rmun argument in mp_plot_abundance to avoid misunderstanding. (2023-08-18, Fri)
https://github.com/YuLab-SMU/MicrobiotaProcess/issues/99mp_import_humann_regroup() to keep the abundance of contributed taxa in each sample
with keep.contribute.abundance=TRUE. (2023-08-15, Tue)rlang::check_installed() to check if a suggested package is installed, which will offer to
install the package before continuing. (2023-08-02, Wed)order.by.feature argument in mp_plot_abundance to adjust the sample order. (2023-07-24, Mon)citation and suppress the message introduced by tidytree. (2023-07-14, Fri)mp_plot_ord to display the result of mp_adonis with show.adonis = TRUE. (2023-06-21, Wed)theme_blinds of ggfun. (2023-06-20, Tue)mp_import_humann_regroup function to parsing the output of humann_regroup_table. (2023-05-15, Mon)fortify method for MPSE object. (2023-05-18, Thu)force = TRUE and relative = FALSE. (2023-04-28, Fri)ggdiffclade using the geom layer of ggtree. (2023-03-02)mp_cal_dist to support storing the distance between the features with action='add'. (2023-03-28)mp_diff_analysis. (2023-04-11)mp_plot_diff_res and mp_plot_diff_boxplot to support visualize the abundance (not
relative abundance). (2022-12-02, Fri)tip.label and rownames of assays when tree is provided in mp_import_dada2 (2022-12-02, Fri)mp_diff_analysis. (2022-12-06, Tue)left_join. (2022-12-15, Thu)mp_plot_abundance to be compatible with the latest ggplot2. (2022-11-08, Tue)mp_plot_diff_manhattan to visualize the different results with manhattan plot. (2022-11-21, Mon)mp_plot_diff_boxplot and update mp_plot_abundance. (2022-10-27, Thu)mp_plot_diff_boxplot. (2022-10-18, Tue)dtplyr. (2022-10-14, Fri)mp_plot_diff_res to support the custom DAA results. (2022-09-27, Tue)show method of MPSE to avoid the colname advice. (2022-09-27, Tue)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)mp_cal_dist to support specifying distmethod to a function. (2022-09-20, Tue)left_join to support joining the dist class. (2022-09-20, Tue)mp_plot_diff_boxplot when taxatree slot is NULL. (2022-08-22, Mon)mp_import_biom to build MPSE class from biom-format file. (2022-07-13, Wed)ggdiffbox. (2022-07-29, Fri)mp_plot_diff_cladogram. (2022-05-25)mp_plot_diff_cladogram in vignetters. (2022-05-14)chunks in mp_plot_rarecurve. (2022-05-14)rm.zero argument in mp_plot_abundance to control whether mask the zero abundance of species. (2022-05-06)taxa.class argument in mp_diff_analysis to test the specified taxa level. (2022-04-28)mp_plot_diff_cladogram to plot the result of mp_diff_analysis. (2022-04-19)mp_aggregate_clade and mp_balance_clade. (2022-04-13)mp_cal_pd_metric to calculate the related phylogenetic diversity metrics. (2022-04-02)
including NRI, NTI, PD, PAE, HAED, EAED, IAC.mp_balance_clade to calculate the balance score of internal nodes according to their tip nodes abundances. (2022-03-22)extract_binary_offspring to find the descendant tip/internal/all (with type parameter) nodes. (2022-03-17)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)mp_select_as_tip and fix the bug of mp_diff_analysis with specific tip.level (not OTU) argument. (2022-03-02, Mon)replace_na bug of new tidyr. (2022-03-04, Fri)mp_import_metaphlan to better parse the output of MetaPhlAn2. (2022-03-11, Fri)mp_cal_abundance to return the tbl_df contained numeric type sample metadata. (2022-03-11, Fri).group of mp_plot_alpha. (2022-02-15, Tue).group of mp_plot_abundance when plot.group=TRUE. (2022-02-14, Mon)width of mp_plot_abundance with geom="flowbar". (2022-02-01, Tue)lda of MASS (2022-01-27, Thu)kingdom level of taxonomy
information contains k__ or K__, which is unknown annotation in kingdom. (2021-01-14, Fri)mp_extract_taxatree and mp_extract_otutree (alias of mp_extract_tree). (2022-01-14, Fri)mp_cal_alpha. (2021-12-31, Fri)bar option in mp_plot_abundance, default is flowbar, the other options are bar and heatmaphopach. (2021-12-27, Mon)tax_table without required phyloseq. (2021-12-20, Mon)mp_diff_analysis to support the factor type group (.group specified). (2021-12-20, Mon)taxatree<- and otutree<- which will extract the intersection between the
tip labels of input treedata and the rownames of MPSE. (2021-12-14, Tue)taxonomy<- for MPSE to assign the taxonomy information, which will be
converted to taxatree automatically. (2021-12-14, Tue)tax_table for MPSE and return taxonomyTable defined in phyloseq. (2021-12-14, Tue)mp_import_metaphlan to better parse the output of MetaPhlAn2. (2021-11-30, Tue)heatmap by setting geom..group supports multiple characters
and .sec.group will be removed in
the next version.mp_plot_diff_res (2021-11-23, Tue)
otutree and taxatree class by setting tree.type.layout.offset.abun, pwidth.abun, offset.effsize, pwidth.effsizegroup
instead of sample by setting group.abun=TRUE or
sample number > 50mp_plot_diff_res to visualize the result of mp_diff_analysis. (2021-11-22, Mon)mp_cal_abundance, mp_cal_venn and mp_cal_upset with dtplyr. (2021-11-18, Thu)ggside in mp_plot_ord. (2021-11-15, Mon)mp_plot_abundance to visualize the abundance of taxonomy from high
(bottom) to low (top). (2021-11-15, Mon)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)select. (2021-11-09, Tue)print for MPSE class. (2021-11-09, Tue)otutree<- for support phylo class. (2021-11-09, Tue)mp_cal_dist result with action="add". (2021-11-09, Tue)as.MPSE for biom class to support parsing the metadata of sample. (2021-11-09, Tue)filter only return a assays contained one feature (nrow=1). (2021-11-05, Fri)rownames<- when rownames of MPSE is NULL. (2021-11-04, Thu)mp_cal_alpha, mp_cal_venn, mp_cal_upset, mp_cal_abundance
and mp_cal_NRT_NTI. (2021-10-29, Fri).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)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)trimSample in mp_rrarefy to check whether to remove the samples that
do not have enough abundance. (2021-10-11, Mon)MPSE to allow assays supporting data.frame or DFrame class. (2021-10-08, Fri)mp_plot_ord to suppress the message of the third depend package. (2021-10-08, Fri)AsIs list class in unnest for the tidyr (>= 1.1.4). (2021-10-01, Fri)mp_aggregate function. (2021-09-26, Sun)mp_plot_upset. (2021-09-10, Fri)mp_plot_ord. (2021-09-13, Mon)matrix to compatible with DESeqDataSet
of DESeq2, test_differential_abundance of tidybulk. (2021-09-09, Thu)show and print for format output of MPSE class. (2021-09-08, Wed)mp_cal_abundance use new tidytree. (2021-09-07, Tue)include.lowest parameter in mp_filter_taxa. (2021-09-07, Tue)mp_plot_ord to display the bioplot for result of cca, rda and envfit. (2021-09-06, Mon)MicrobiotaProcess. (2021-09-04, Sat)MPSE object after the mp_diff_analysis is done with action="add". (2021-08-31, Fri)
taxtree and otutree with the result of different analysis can be extracted with mp_extract_tree.print for one line of MPSE and update mp_plot_ord to display the side boxplot. (2021-08-31, Tue)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)mp_plot_dist for MPSE or tbl_mpse object after mp_cal_dist is performed with action="add". (2021-08-28, Sat)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)rowname or colnames of SummarizedExperiment is NULL for as.MPSE. (2021-08-26, Thu)rownames of assays and colnames of colData to identical for SummarizedExperiment(1.23.3). (2021-08-26, Thu)mp_extract_refseq for MPSE object. (2021-08-25, Wed)as.MPSE for SummarizedExperiment object. (2021-08-24, Tue)mp_filter_taxa to drop the taxa that low abundance and low occurrences. (2021-08-24, Tue)colData<- and left_join for MPSE. (2021-08-23, Mon)mutate for MPSE object.parse_taxonomy_greengenes and parse_taxonomy_qiime from phyloseq. (2021-08-17, Tue)as.MPSE for TreeSummarizedExperiment class. (2021-08-17, Tue)mp_import_metaphlan to parsing the output of MetaPhlAn. (2021-08-12, Thu)
treefile argument to import the tree of MetaPhlAn3 (mpa_v30_CHOCOPhlAn_201901_species_tree.nwk) (2021-08-13, Fri)print of MPSE object via pillar package. (2021-08-06, Fri)mp_extract_dist by introducing .group argument to return a tbl_df for
visualization. (2021-08-04, Wed)taxatree, taxatree<-, otutree, otutree<-, refseq, refseq<- for MPSE. (2021-08-04, Wed)mp_extract_rarecurve to extract the result of mp_cal_rarecurve from
MPSE or tbl_mpse object. (2021-08-04, Wed)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)mp_extract_abundance to mp_extract_assays from MPSE or tbl_mpse. (2021-07-31, Sat)mp_cal_clust by introducing action argument. (2021-07-29, Thu).as.phyloseq for MPSE or tbl_mpse object. (2021-07-28, Wed)mp_diff_analysis for MPSE or tbl_mpse object. (2021-07-27, Tue)dr_extract for the visualization of the result of ordination. (2021-07-26, Mon)phyloseq and add rd of the function for MPSE or tbl_mpse. (2021-07-24, Sat)rda, cca, envfit. (2021-07-23, Fri)tidydr to convert the result of reduce dimension to tbl_df
pca, pcoa, nmds, rda, cca. (2021-07-22, Thu)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)
as.MPSE to convert phyloseq or tbl_mpse to MPSE class.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.
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)clustplotClass to treedata. (2021-06-28, Tue)mp_rrarefy method to rarefy species richness. (2021-06-29, Tue)
MPSE, tbl_mpse, grouped_df_mpse object via wrapping vegan::rrarefy.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 slotellipse_linewd and ellipse_lty in ggordpoint to control
the width and line type of ellipse line. (2021-05-24, Mon)diff_analysis. (2021-06-06, Sun)filter function to filter the result of diff_analysis. (2021-06-07, Mon)diff_analysis. (2021-06-07, Mon)
headtail[[[]]$dimget_NRI_NTI to calculate the NRI and NTI. (2021-06-08, Tue)ggclust bug to map color and shape. (2021-05-12, Wed)ggdiffclade. (2021-04-16, Fri)ggbartaxa and ggdiffbartaxa. (2021-03-23, Tue)sampleLevels in ggbartax to adjust the order of axis label. (2021-03-12, Fri)import_qiime2 to avoid error when only feature table is provided. (2021-02-26, Fri)svg dev to pdf dev. (2021-02-04, Thu)ggrarecurve. (2021-01-07, Thu)
factorNames="Group" to factorNames="group"geom_tiplab also support circular layout, so remove geom_tiplab2. (2020-11-26, Thu)as.treedata for taxonomyTable class. (2020-11-23, Mon)ggrarecurve can be set color with variable of group for each samples. (2020-11-11, Tue)
shadow=FALSE and providing factorNamesget_rarecurve to avoid repeated calculation when displaying rare curve. (2020-11-17, Tue)
rareres <- get_rarecurve(obj, chunks=400)
p <- ggrarecurve(rareres)ggordpoint add showsample to show the labels of sample. (2020-10-29, Thu)ggordpoint use the points of ggstar. (2020-10-30, Fri)diff_analysis, the call was changed to someparams.
someparams contained the arguments used in other functions. (2020-11-09, Mon)
retrieve_seq and mapply_retrieve_seq function, since these need internet.
Which might cause time out when check. (2020-10-16, Fri)tax_table(ps) to ps@tax_table to
avoid generate error when tax_table is NULL. (2020-10-15, Thu)drop_taxa. (2020-10-14, Wed)ggdiffclade to support data.frame input when reduce is TRUE. (2020-08-28, Fri)ggordpoint to fit the usage when user want to set mapping by manually. (2020-08-25, Tue)get_taxadf, get_alltaxadf and diff_analysis has supported function datasets or other type datasets. (2020-08-17, Mon)cladetext argument has been omitted in ggdiffclade, now it has been fixed. (2020-08-14, Fri)size argument controlled the width of line of tree has been deprecated.
The linewd replace it (2020-08-14, Fri).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)inward_circular layout in ggdiffclade. (2020-08-12, Wed)ggdifftaxbar supports png, tiff format. (2020-08-10, Mon)diff_analysis. (2020-08-10, Mon)tax_table information to result of get_taxadf. (2020-08-07, Fri)rename_ and group_by_ggdiffclade when layout is slanted or rectangular (2020-08-05, Wed)