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8_pca_analysis.yml
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target_default: 8_pca_analysis
packages:
- pah
- httr
- ggplot2
- dplyr
- remake
- sf
- USAboundaries
include:
- 7_double_ratios.yml
sources:
- 8_pca_analysis/src/pca_top_sources.R
- 8_pca_analysis/src/map_pca.R
targets:
8_pca_analysis:
depends:
- pca_creosote
- pca_no_creosote
- pca_top_sources_bysite
- pca_top_sources
- 8_pca_analysis/doc/pca_components_plot_creosote.png
- 8_pca_analysis/doc/pca_components_plot_nocreosote.png
- 8_pca_analysis/doc/pca_boxplot_creosote.png
- 8_pca_analysis/doc/pca_boxplot_nocreosote.png
- 8_pca_analysis/doc/map_closestsource_bysite.png
- 8_pca_analysis/doc/pca_components_plot_creosote.pdf
- 8_pca_analysis/doc/pca_components_plot_nocreosote.pdf
- 8_pca_analysis/doc/pca_boxplot_creosote.pdf
- 8_pca_analysis/doc/pca_boxplot_nocreosote.pdf
- 8_pca_analysis/doc/map_closestsource_bysite.pdf
pca_creosote:
command: pah_pca(profiles = profiles, perc_cutoff = 10, sample_column = I("unique_id"))
pca_no_creosote:
command: pah_pca(profiles = profiles_nocreosote, perc_cutoff = 10, sample_column = I('unique_id'))
pca_top_sources_bysite:
command: get_pca_top_sources(pca_dat = pca_no_creosote)
pca_top_sources:
command: get_pca_top_sources_simple(pca_dat = pca_no_creosote)
8_pca_analysis/doc/pca_components_plot_creosote.png:
command: plot_pca(pca_creosote, plot_type = I('pca_components'))
plot: {width: 10, height: 10, unit: 'in', res: 400}
8_pca_analysis/doc/pca_components_plot_nocreosote.png:
command: plot_pca(pca_no_creosote, plot_type = I('pca_components'))
plot: {width: 10, height: 10, unit: 'in', res: 400}
8_pca_analysis/doc/pca_boxplot_creosote.png:
command: plot_pca(pca_creosote, plot_type = I('distance_boxplot'), source_abbreviation = FALSE)
plot: {width: 3.64, height: 4, unit: 'in', res: 400}
8_pca_analysis/doc/pca_boxplot_nocreosote.png:
command: plot_pca(pca_no_creosote, plot_type = I('distance_boxplot'), source_abbreviation = FALSE)
plot: {width: 3.64, height: 4, unit: 'in', res: 400}
8_pca_analysis/doc/map_closestsource_bysite.png:
command: make_map_pca(sample_info = samples, pca_dat = pca_top_sources_bysite, conc_dat = prepped_totals)
plot: {width: 10, height: 6, unit: 'in', res: 400}
8_pca_analysis/doc/pca_components_plot_creosote.pdf:
command: plot_pca(pca_creosote, plot_type = I('pca_components'))
plot: {width: 10, height: 10}
8_pca_analysis/doc/pca_components_plot_nocreosote.pdf:
command: plot_pca(pca_no_creosote, plot_type = I('pca_components'))
plot: {width: 10, height: 10}
8_pca_analysis/doc/pca_boxplot_creosote.pdf:
command: plot_pca(pca_creosote, plot_type = I('distance_boxplot'), source_abbreviation = FALSE)
plot: {width: 3.64, height: 4}
8_pca_analysis/doc/pca_boxplot_nocreosote.pdf:
command: plot_pca(pca_no_creosote, plot_type = I('distance_boxplot'), source_abbreviation = FALSE)
plot: {width: 3.64, height: 4}
8_pca_analysis/doc/map_closestsource_bysite.pdf:
command: make_map_pca(sample_info = samples, pca_dat = pca_top_sources_bysite, conc_dat = prepped_totals)
plot: {width: 10, height: 6}