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fix issues preventing social-epi vignette from knitting #12

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merged 2 commits into from
Sep 7, 2023
Merged

fix issues preventing social-epi vignette from knitting #12

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9ada3ef
fix issues preventing vignette from knitting
cmirzayi Jun 29, 2023
081e7d3
removed devtools call that was causing build errors
cmirzayi Jun 30, 2023
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2 changes: 1 addition & 1 deletion R/diversity_plots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ plot_alpha_by <- function(pseq, vars, metadata=sample_data(pseq)[,vars], notch=T
df_alpha$id <- seq_len(nrow(df_alpha))


melt_alpha <- na.omit(melt(df_alpha, measure.vars = measure.vars, id.vars="id"))
melt_alpha <- na.omit(reshape2::melt(df_alpha, measure.vars = measure.vars, id.vars="id"))
melt_alpha %<>% left_join(dplyr::select(df_alpha, id, Chao1), by="id")
#sort levels of each variable in melted form
melt_alpha$value <- factor(melt_alpha$value,
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10 changes: 5 additions & 5 deletions vignettes/social-epi.Rmd
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Expand Up @@ -33,20 +33,20 @@ suppressPackageStartupMessages({
library(dplyr)
library(magrittr)
library(ggplot2)
#library(nychanesmicrobiome)
devtools::load_all()
library(nychanesmicrobiome)
#devtools::load_all()
})
```


```{r load_data}
#full NYC-HANES2 dataset
nychanes_sas <- sas7bdat::read.sas7bdat("http://nychanes.org/wp-content/uploads/sites/6/2015/11/NYCHANES_2013_14_V2_09212016.sas7bdat")
nychanes_sas <- sas7bdat::read.sas7bdat("https://med.nyu.edu/departments-institutes/population-health/divisions-sections-centers/epidemiology/sites/default/files/nyc-hanes-datasets-and-resources-analytic-data-sets-sas-file.sas7bdat")
nychanes_full <- annotateFullDataset(nychanes_sas)

#pilot microbiome data
suppressPackageStartupMessages({
NYC_HANES_raw <- loadQiimeData(nychanes_sas)
NYC_HANES_raw <- loadQiimeData()
NYC_HANES <- annotateFactors(NYC_HANES_raw)
})
metadata <- data.frame(sample_data(NYC_HANES))
Expand Down Expand Up @@ -668,7 +668,7 @@ sessionInfo()
```

```{r check_n_otus_smoking}
alt_smokers_cigarettes <- sample_data(NYC_HANES) %>% dplyr::filter(smokingstatus == 'Alternative smoker') %>% dplyr::filter(CIGARETTES == 'Yes') %>% dplyr::select(Burklab_ID) %>% t
alt_smokers_cigarettes <- sample_data(NYC_HANES) %>% data.frame() %>% dplyr::filter(smokingstatus == 'Alternative smoker') %>% dplyr::filter(CIGARETTES == 'Yes') %>% dplyr::select(Burklab_ID) %>% t
NYC_HANES <- prune_samples(!(sample_names(NYC_HANES) %in% alt_smokers_cigarettes), NYC_HANES)
sample_data(NYC_HANES)$smokingstatus <- relevel(sample_data(NYC_HANES)$smokingstatus,"Never smoker")

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