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NAMESPACE
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NAMESPACE
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# Exports for JMDplots package
export(
# gradox paper 20190928
"gradox1", "gradox2", "gradoxS1", "gradoxS2", "gradox3", "gradox4", "gradox5",
# chnosz10 paper 20190929
"chnosz101", "chnosz104", "chnosz105", "chnosz106", "chnosz107",
"chnosz10S1", "chnosz10S2", "chnosz10S3", "chnosz10S5",
"chnosz10S6A", "chnosz10S6B", "chnosz10S7", "chnosz10S8", "chnosz10S9", "chnosz10S10",
# gradH2O paper 20190930-20191008, 20191104, 20191117, 20200421, 20200821, 20200826
"gradH2O0", "gradH2O1", "gradH2O2", "gradH2O3", "gradH2O4",
"gradH2O5", "gradH2O6", "gradH2O7",
# grad_mplot 20190930
"mplot", "mpage", "ppage", "mcomp", "pcomp",
# Nif-encoding genomes 20191015
"NifProteomes",
# aoscp paper 20191018
"aoscp1", "aoscp2", "aoscp3", "aoscp4", "aoscp5", "aoscp6",
"yeast.aa", "yeastgfp", "yeast.ZC",
# scsc paper 20191019
"scsc2", "scsc3",
# aaaq paper 20191020
"aaaq4", "aaaq10", "aaaq13",
# utilities 20191027
"addexif",
# 20191127 (added to canprot), 20220113 (moved to JMDplots)
"PS",
# canH2O paper 20200203-20200204
"canH2O1", "pdat_HPA", "pdat_TCGA", "canH2O2", "canH2O3", "canH2O4",
# canH2O supplementary tables and figures 20200205
"canH2OT1", "canH2OT2", "canH2OS1", "canH2OS2",
# canH2O paper 20200420
"pdat_osmotic_gene", "pdat_aneuploidy",
# 20200508
"pdat_yeast_stress",
# Bison Pool papers 20200712
"bison1", "bison2", "bison3", "bison4",
"bison5", "bison6", "bison7", "bison8",
# JMDplots package data 20200828
"JMDplots",
# cpcp plots 20201015
"Ehplot", "rankdiff", "rankplot", "groupplots", "mergedplot", "get_colors",
# evdevH2O paper 20210127
"evdevH2O2", "evdevH2O4", "evdevH2O5", "evdevH2O6", "evdevH2O7", "evdevH2O8",
"MaximAct", "runMaximAct", "LYSC_example",
"getphyloaa", "getCBS17", "getFOK21", # 20210706-20210708
"evdevH2O3", # 20211222
"evdevH2O1", # 20220216
# mjenergy paper 20210205
"mjenergy1", "mjenergy2", "mjenergy3", "calc_affinity",
"mjenergy_Table_S3", "mjenergy_Dataset_S1", # 20210816
# evdevH2O paper 20210402
"pdat_fly",
# geo16S paper 20210416-20210610
"geo16S1", "geo16S2", "geo16S3", "geo16S4",
"geo16S5", # 20211018
"geo16S_S1", "geo16S_S2", # 20220105
"geo16S_S3", # 20220112
"geo16S_S4", # 20220117
"geo16S_S5", # 20220114
"geo16S_S6", # 20220126
# orp16S paper 20211003-20211008
"orp16S_3", "orp16S_4", "orp16S_5", "orp16S_6", "orp16S_S1",
"plotEZ", "plotMA",
# utogig paper 20220420
"utogig1", "utogig2", "utogig3", "utogigS2", "utogigS4", "calc_logaH2_intermediate",
# Moving functions to chem16S package 20220506-20220513
"getmdat_geo16S", "getmetrics_geo16S", "plotmet_geo16S", "getmdat_orp16S", "getmetrics_orp16S", "orp16S_info",
# orp16S paper 20220516-20220517
"orp16S_T1", "orp16S_S2",
# utogig paper 20220602, 20220605
"utogig4", "utogigS1",
# utilities 20220930
"hyphen.in.pdf",
# orp16S paper 20221001
"orp16S_D3",
# orp16S paper 20221230
"orp16S_1", "orp16S_2",
# microhum paper 20230212
"microhum_3", "microhum_4", "microhum_6", "dataset_metrics",
# chem16S paper 20230709
"chem16S_1",
# microhum paper 20230212
"microhum_3_1", "microhum_5_1",
# microhum paper 20231222
"microhum_1", "microhum_1_1",
# microhum paper 20231227, 20231231, 20240212
"microhum_5", "microhum_2", "microhum_6_1",
# function used in geo16S and microhum 20231231
"plot_starburst",
# carrollite paper 20240205
"calc_carrollite", "add_Co_aqueous", "carrollite_5", "carrollite_8",
"carrollite_S3", "carrollite_S4", "carrollite_S5", "carrollite_S6",
## Moved from canprot 20240226
"pdat_colorectal",
"pdat_pancreatic", "pdat_hypoxia",
## 20191226-20191230
".pdat_multi", "pdat_secreted", "pdat_breast", "pdat_lung", "pdat_prostate", "pdat_3D",
## 20200402, 20200411
"pdat_liver", "pdat_glucose",
## 20200414
"mkvig",
## 20200418
".pdat_osmotic", "pdat_osmotic_bact", "pdat_osmotic_euk", "pdat_osmotic_halo",
"check_IDs", "cleanup", "get_comptab", "diffplot", "qdist",
"xsummary", "xsummary2", "xsummary3",
# genoGOE paper 20240328, 20240409, 20240602
"genoGOE_2", "genoGOE_3", "genoGOE_1"
)
# Imports from CHNOSZ
importFrom("CHNOSZ",
# first batch: gradox
"ZC", "affinity", "aminoacids", "as.chemical.formula",
"basis", "diagram", "info", "label.figure", "makeup",
"species", "swap.basis", "thermo", "thermo.axis", "mod.OBIGT",
# second batch: chnosz10
"axis.label", "bgamma", "describe.basis", "describe.property",
"describe.reaction", "equilibrate", "expr.property", "expr.species",
"list2array", "mass", "mod.buffer", "mosaic",
"nonideal", "ratlab", "reset", "solubility",
"subcrt", "thermo.plot.new", "water", "OBIGT", "add.OBIGT",
# third batch: gradH2O
"protein.formula", "protein.basis",
# fourth batch: aoscp
"convert", "protein.length", # read.fasta() moved to canprot::read_fasta()
# fifth batch: scsc
"add.protein", "label.plot", # aasum() moved to canprot::sum_aa()
# sixth batch: aaaq
"water.lines", "pinfo", "ionize.aa",
# cpcp
"palply",
# evdevH2O
"protein.OBIGT", "syslab",
# mjenergy
"E.units",
# utogig
"rank.affinity",
# carrollite
"logB.to.OBIGT", "T.units", "check.GHS", "retrieve", "stack_mosaic",
"lT", "lP", "lNaCl", "lS", "lex"
)
# Imports from canprot
importFrom("canprot",
# first batch: gradH2O1 20190930
"canprot",
# moved from JMDplots to canprot 20191027
"Zc", "nH2O", "GRAVY", "pI",
# for pdat_* functions 20200204
"human_aa",
# for canH2O5() 20200505, 20200508
"cplab",
# for canH2OS1() 20201016
"nO2",
# for get_comptab() 20240227
"CLES",
# moved from CHNOSZ to canprot 20240228
"read_fasta", "sum_aa",
# moved from JMDplots to canprot 20240301, 20240304
"add_cld", "Cost",
# moved from chem16S to canprot 20240302, 20240310
"calc_metrics", "add_hull"
)
# Imports from chem16S
importFrom("chem16S",
# 20220506
"read_RDP", "map_taxa", "get_metrics", "plot_metrics",
# 20230709
"plot_ps_metrics", "plot_ps_metrics2",
# 20230731
"chemlab"
)
# Imports from other packages
importFrom("shiny", "fluidPage", "includeCSS", "shinyApp")
importFrom("timevis", "renderTimevis", "timevis", "timevisOutput")
importFrom("png", "readPNG")
importFrom("MASS", "kde2d")
importFrom("diagram", "openplotmat", "coordinates", "straightarrow", "curvedarrow",
"textrect", "textplain", "textempty")
importFrom("ggplot2", "theme_bw", "xlab", "ylab", "geom_hline", "geom_vline", "theme",
"element_text", "ggplot", "aes", "geom_point", "ggtitle", "labs", "xlim", "ylim",
"theme_void", "geom_text", "annotate", "unit",
"ggplot_gtable", "ggplot_build", "theme_classic", "element_rect", "ggsave",
"geom_smooth", "geom_contour",
"theme_set", "coord_cartesian", "facet_wrap", "geom_line", "geom_polygon", "guides", "guide_legend")
importFrom("grid", "grid.roundrect", "gpar", "grid.draw")
importFrom("oce", "mapPlot", "mapPoints", "mapPolygon")
importFrom("sf", "st_coordinates", "st_read", "st_transform")
importFrom("eulerr", "euler")
importFrom("ape", "read.tree", "plot.phylo", "rotateConstr")
importFrom("multcompView", "multcompLetters4")
importFrom("beanplot", "beanplot")
# We need a method provided by the package, not an exported function, so import the whole package 20211230
import("plot.matrix")
# Imports from standard packages
importFrom("grDevices", "dev.off", "cairo_pdf", "pdf", "blues9", "colorRampPalette",
"chull", "col2rgb", "rgb", "colorRamp", "heat.colors", "topo.colors",
"extendrange", "contourLines", "hcl.colors", "savePlot", "png", "dev.list",
"palette", "palette.colors", "dev.cur", "adjustcolor")
importFrom("graphics", "abline", "arrows", "axis", "box", "layout",
"legend", "lines", "mtext", "par", "plot", "plot.new",
"points", "rect", "text", "title", "smoothScatter", "strheight",
"polygon", "hist", "plot.window", "rasterImage",
"contour", "grconvertX", "grconvertY", "image",
".filled.contour", "Axis", "close.screen", "lcm", "screen",
"split.screen", "boxplot", "matlines", "matplot")
importFrom("stats", "lm", "na.omit", "predict", "sd", "predict.lm", "residuals",
"qqline", "qqnorm", "quantile", "median", "fivenum",
"density", "formula", "t.test", "approx", "splinefun", "xtabs",
"coefficients", "loess", "wilcox.test", "weighted.mean",
"kmeans", "qt", "cor.test", "coef", "aggregate", "cor", "uniroot",
"TukeyHSD", "aov", "binom.test", "confint", "ecdf", "knots")
importFrom("utils", "read.csv", "demo", "tail", "write.csv",
"capture.output", "browseURL", "head", "combn", "read.table",
"data", "relist", "write.table")
S3method(dunnTest,default)
S3method(dunnTest,formula)
S3method(print,dunnTest)
export(dunnTest)