Alpha Diversity
Last updated: 2020-06-17
Checks: 6 1
Knit directory: Fiber_Intervention_Study/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 9da43aa | noah-padgett | 2020-06-08 | Build site. |
| Rmd | 774d405 | noah-padgett | 2020-06-01 | updated glmm and figures |
| html | 774d405 | noah-padgett | 2020-06-01 | updated glmm and figures |
| html | 0733fe5 | noah-padgett | 2020-05-21 | Build site. |
| Rmd | 036301e | noah-padgett | 2020-02-27 | updated alpha analysis |
| html | 036301e | noah-padgett | 2020-02-27 | updated alpha analysis |
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| html | c1bce73 | noah-padgett | 2019-12-11 | Build site. |
| Rmd | db73f64 | noah-padgett | 2019-12-11 | alpha diversity initial analysis |
| html | db73f64 | noah-padgett | 2019-12-11 | alpha diversity initial analysis |
This page contains the investigation of alpha diversity investigations.
Alpha diversity
Boxplots by unique participants
Observed OTUs
p <- ggplot(plot_data, aes(x=SubjectID10, y=Observed,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Observed OTUs")+
guides(colour= guide_legend(title = "Subject ID"))+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
#ggsave("fig/figure1.pdf", p, width=5, height=3.5, units="in")Shannon Index
p <- ggplot(plot_data, aes(x=SubjectID10, y=Shannon,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Shannon Index")+
guides(colour= guide_legend(title = "Subject ID"))+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Simpson
p <- ggplot(plot_data, aes(x=SubjectID10, y=Simpson,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Simpson Index")+
guides(colour= guide_legend(title = "Subject ID"))+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Inverse Simpson
p <- ggplot(plot_data, aes(x=SubjectID10, y=InvSimpson,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Inverse Simpson Index")+
guides(colour= guide_legend(title = "Subject ID"))+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Boxplots by week of study
Observed OTUs
p <- ggplot(plot_data, aes(x=Intervention, y=Observed,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Observed OTUs",
title="Observed OTUs by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Shannon Index
p <- ggplot(plot_data, aes(x=Intervention, y=Shannon,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Shannon Index",
title="Shannon Index by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Simpson
p <- ggplot(plot_data, aes(x=Intervention, y=Simpson,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Simpson",
title="Simpson by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Inverse Simpson
p <- ggplot(plot_data, aes(x=Intervention, y=InvSimpson,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Inverse Simpson",
title="Inverse Simpson by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p
Manuscript Figure
p1 <- ggplot(plot_data, aes(x=SubjectID10, y=Observed,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Observed OTUs",
title="Observed OTUs by Participants")+
guides(colour= guide_legend(title = "Subject ID"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p1
p2 <- ggplot(plot_data, aes(x=Intervention, y=Observed,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Observed OTUs",
title="Observed OTUs by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p2 
p3 <- ggplot(plot_data, aes(x=SubjectID10, y=Shannon,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Shannon Index",
title="Shannon Index by Participants")+
guides(colour= guide_legend(title = "Subject ID"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p3
p4 <- ggplot(plot_data, aes(x=Intervention, y=Shannon,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Shannon Index",
title="Shannon Index by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p4
p5 <- ggplot(plot_data, aes(x=SubjectID10, y=InvSimpson,
colour=SubjectID10, shape=Week))+
geom_point(size=3) +
facet_grid(.~Intervention2, scales = "free")+
labs(x="Subject ID", y= "Inverse Simpson",
title="Inverse Simpson by Participants")+
guides(colour= guide_legend(title = "Subject ID"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p5
p6 <- ggplot(plot_data, aes(x=Intervention, y=InvSimpson,
colour=Intervention,
group=Intervention))+
geom_boxplot(outlier.shape=NA)+
geom_point(size=3, position="jitter")+
facet_wrap(.~Week, nrow=1)+
labs(x=NULL, y="Inverse Simpson",
title="Inverse Simpson by Study Week")+
guides(colour= guide_legend(title = "Intervention"))+
scale_colour_manual(values = cols)+
theme(panel.grid = element_blank(),
strip.text.x = element_text(angle = 0, size = 11, face = "italic"),
axis.text.y = element_text(size = 10),
axis.title = element_text(size = 10),
plot.title = element_text(hjust = 0.5),
axis.title.x = element_blank(),
strip.background = element_blank(),
legend.position = "right",
#legend.text = element_text(size = 7),
#legend.title = element_blank(),
panel.spacing.x=unit(0.001, "lines"))
p6
library(cowplot)
p1.leg <- get_legend(p1)
p2.leg <- get_legend(p2)
p1.nl <- p1 + theme(legend.position = "none", plot.title = element_blank(), axis.text.x = element_blank(), axis.ticks.x = element_blank())
p2.nl <- p2 + theme(legend.position = "none", plot.title = element_blank(), axis.text.y = element_blank(),axis.text = element_blank(), axis.title = element_blank(), axis.ticks = element_blank())
p3.nl <- p3 + theme(legend.position = "none", plot.title = element_blank(), axis.text.x = element_blank(), axis.ticks.x = element_blank(), strip.text.x = element_blank())
p4.nl <- p4 + theme(legend.position = "none", plot.title = element_blank(), axis.text.y = element_blank(), axis.text.x = element_blank(), axis.title.y = element_blank(), axis.ticks = element_blank(), strip.text.x = element_blank())
p5.nl <- p5 + theme(plot.title = element_blank(), strip.text.x = element_blank(), legend.position="none")
p6.nl <- p6 + theme(plot.title = element_blank(), axis.text.y = element_blank(), axis.title.y = element_blank(), axis.ticks.y = element_blank(), strip.text.x = element_blank(), legend.position="none")
p <- p1.nl + p2.nl + p3.nl + p4.nl + p5.nl + p6.nl + plot_layout(nrow=3, ncol=2)
p
ggsave("fig/figure1.pdf", p, width=7.9,height=5, units="in")
#bigplotlegend <- plot_grid(p1.leg, p2.leg, nrow =1, align = "h")
#save_plot("fig/figure1_legend.pdf", bigplotlegend, base_width = 13.25, base_height = 5)Intervention Effect
Overall Effect
Observed OTUs
ggplot(plot_data, aes(x=Intervention, y=Observed))+
geom_boxplot(outlier.alpha = 0,
aes(group=Intervention, color=Intervention))+
geom_point(position="jitter",aes(color=Intervention))+
guides(colour= guide_legend(title = "Intervention"))+
labs(x="Intervention Group")+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
Shannon Index
ggplot(plot_data, aes(x=Intervention, y=Shannon))+
geom_boxplot(outlier.alpha = 0,
aes(group=Intervention, color=Intervention))+
geom_point(position="jitter",aes(color=Intervention))+
guides(colour= guide_legend(title = "Intervention"))+
labs(x="Intervention Group")+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
Simpson
ggplot(plot_data, aes(x=Intervention, y=Simpson))+
geom_boxplot(outlier.alpha = 0,aes(group=Intervention, color=Intervention))+
geom_point(position="jitter",aes(color=Intervention))+
guides(colour= guide_legend(title = "Intervention"))+
labs(x="Intervention Group")+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
Changes Over Time
Observed OTUs
ggplot(plot_data, aes(x=Intervention, y=Observed,
group=Intervention,
color=Intervention, shape=Intervention))+
geom_boxplot(outlier.alpha = 0)+
geom_point(position="jitter")+
facet_grid(.~Week)+
labs(x="Intervention Group by Week")+
guides(colour= guide_legend(title = "Intervention"))+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
ggplot(plot_data, aes(x=Week, y=Observed,
group=interaction(Intervention, SubjectID3),
color=SubjectID3, shape=Intervention))+
#geom_boxplot(outlier.alpha = 0)+
geom_point()+
geom_line()+
#facet_grid(.~Week)+
labs(x="Intervention Group by Week")+
guides(colour= guide_legend(title = "Intervention"))+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
Shannon Index
ggplot(plot_data, aes(x=Intervention, y=Shannon,
group=Intervention,
color=Intervention, shape=Intervention))+
geom_boxplot(outlier.alpha = 0)+
geom_point(position="jitter")+
facet_grid(.~Week)+
labs(x="Intervention Group by Week")+
guides(colour= guide_legend(title = "Intervention"))+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
Simpson
ggplot(plot_data, aes(x=Intervention, y=Simpson,
group=Intervention,
color=Intervention, shape=Intervention))+
geom_boxplot(outlier.alpha = 0)+
geom_point(position="jitter")+
facet_grid(.~Week)+
labs(x="Intervention Group by Week")+
guides(colour= guide_legend(title = "Intervention"))+
theme(axis.text.x = element_text(angle = 0, hjust=0.33))
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cowplot_1.0.0 microbiome_1.8.0 car_3.0-8 carData_3.0-4
[5] gvlma_1.0.0.3 patchwork_1.0.0 viridis_0.5.1 viridisLite_0.3.0
[9] gridExtra_2.3 xtable_1.8-4 kableExtra_1.1.0 plyr_1.8.6
[13] data.table_1.12.8 readxl_1.3.1 forcats_0.5.0 stringr_1.4.0
[17] dplyr_0.8.5 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0
[21] tibble_3.0.1 ggplot2_3.3.0 tidyverse_1.3.0 lmerTest_3.1-2
[25] lme4_1.1-23 Matrix_1.2-18 vegan_2.5-6 lattice_0.20-38
[29] permute_0.9-5 phyloseq_1.30.0
loaded via a namespace (and not attached):
[1] Rtsne_0.15 minqa_1.2.4 colorspace_1.4-1
[4] rio_0.5.16 ellipsis_0.3.1 rprojroot_1.3-2
[7] XVector_0.26.0 fs_1.4.1 rstudioapi_0.11
[10] farver_2.0.3 fansi_0.4.1 lubridate_1.7.8
[13] xml2_1.3.2 codetools_0.2-16 splines_3.6.3
[16] knitr_1.28 ade4_1.7-15 jsonlite_1.6.1
[19] workflowr_1.6.2 nloptr_1.2.2.1 broom_0.5.6
[22] cluster_2.1.0 dbplyr_1.4.4 BiocManager_1.30.10
[25] compiler_3.6.3 httr_1.4.1 backports_1.1.7
[28] assertthat_0.2.1 cli_2.0.2 later_1.0.0
[31] htmltools_0.4.0 tools_3.6.3 igraph_1.2.5
[34] gtable_0.3.0 glue_1.4.1 reshape2_1.4.4
[37] Rcpp_1.0.4.6 Biobase_2.46.0 cellranger_1.1.0
[40] vctrs_0.3.0 Biostrings_2.54.0 multtest_2.42.0
[43] ape_5.3 nlme_3.1-144 iterators_1.0.12
[46] xfun_0.14 openxlsx_4.1.5 rvest_0.3.5
[49] lifecycle_0.2.0 statmod_1.4.34 zlibbioc_1.32.0
[52] MASS_7.3-51.5 scales_1.1.1 hms_0.5.3
[55] promises_1.1.0 parallel_3.6.3 biomformat_1.14.0
[58] rhdf5_2.30.1 curl_4.3 yaml_2.2.1
[61] stringi_1.4.6 S4Vectors_0.24.4 foreach_1.5.0
[64] BiocGenerics_0.32.0 zip_2.0.4 boot_1.3-24
[67] rlang_0.4.6 pkgconfig_2.0.3 evaluate_0.14
[70] Rhdf5lib_1.8.0 labeling_0.3 tidyselect_1.1.0
[73] magrittr_1.5 R6_2.4.1 IRanges_2.20.2
[76] generics_0.0.2 DBI_1.1.0 foreign_0.8-75
[79] pillar_1.4.4 haven_2.3.0 whisker_0.4
[82] withr_2.2.0 mgcv_1.8-31 abind_1.4-5
[85] survival_3.1-8 modelr_0.1.8 crayon_1.3.4
[88] rmarkdown_2.1 grid_3.6.3 blob_1.2.1
[91] git2r_0.27.1 reprex_0.3.0 digest_0.6.25
[94] webshot_0.5.2 httpuv_1.5.2 numDeriv_2016.8-1.1
[97] stats4_3.6.3 munsell_0.5.0