In philippmuench/PMtools: Miscellaneous helper functions

Figure 5

Order of sites:

1. Supragingival_plaque
2. Buccal_mucosa
3. Tongue_dorsum
4. Stool
5. Anterior_nares
6. R_Retroauricular_crease
7. Posterior_fornix

library(PMtools)
data(humann2_table)
data(hmp1_2_metadata)
data(hmp1_2_metaphlan)

# generate the sample order
custom.order <-
  orderHumannBySimilarity(hmp1_2_metaphlan, distance.method = "bray")

p <- NULL
cas_plots <- vector('list', 10)
plot.colors <- NULL
sample.threshold <- 30

for (cas in paste0("Cas", 1:10)) {
  cas_plots[[cas]]  <- local({

 dat <-
      humann2Barplot(
        humann2_table,
        metadata = hmp1_2_metadata,
        feature = cas,
        num.bugs = "auto",
        metadata.factor = 5,
        column.stratification.order =  c("Subgingival_plaque","Supragingival_plaque","Buccal_mucosa","Saliva","Tongue_dorsum","Throat","Hard_palate","Keratinized_gingiva","Palatine_Tonsils","Stool","Anterior_nares","L_Retroauricular_crease","R_Retroauricular_crease","R_Antecubital_fossa","Mid_vagina","Posterior_fornix","Vaginal_introitus"),
        num.bugs.explained.fraction = 0.35,
        order.by = "custom",
        custom.order = custom.order,
      )

    p <-
      makeHumann2Barplot(
        dat,
        last.plot.colors = NULL,
        hide.legend = F,
        sample.threshold = sample.threshold,
        fixed.floor = -1,
        fixed.ymax = 3,
        scale = "proportional-log",
        space = "fixed"
        )
     plot.colors <<- rbind(plot.colors, p$colors)
  })
}

# use plot colors for plotting
cas_plots <- vector('list', 10)

for (cas in paste0("Cas", 1:10)) {
  cas_plots[[cas]]  <- local({

 dat <-
      humann2Barplot(
        humann2_table,
        metadata = hmp1_2_metadata,
        feature = cas,
        num.bugs = "auto",
        metadata.factor = 5,
        column.stratification.order =  c("Subgingival_plaque","Supragingival_plaque","Buccal_mucosa","Saliva","Tongue_dorsum","Throat","Hard_palate","Keratinized_gingiva","Palatine_Tonsils","Stool","Anterior_nares","L_Retroauricular_crease","R_Retroauricular_crease","R_Antecubital_fossa","Mid_vagina","Posterior_fornix","Vaginal_introitus"),
        num.bugs.explained.fraction = 0.35,
        order.by = "custom",
        custom.order = custom.order,
        last.plot.colors = plot.colors
      )

    p <-
      makeHumann2Barplot(
        dat,
        last.plot.colors = plot.colors,
        hide.legend = F,
        fixed.floor = -1,
        sample.threshold = sample.threshold,
        fixed.ymax = 3,
        scale = "proportional-log",
        space = "fixed",
        hide.strata.legend = T
        )
  })
}

pdf("figure6_no_legend.pdf", height = 10, width = 9)
print(multiplot(plotlist = cas_plots, cols = 2))
dev.off()

# use plot colors for plotting
cas_plots <- vector('list', 10)

for (cas in paste0("Cas", 1:10)) {
  cas_plots[[cas]]  <- local({

 dat <-
      humann2Barplot(
        humann2_table,
        metadata = hmp1_2_metadata,
        feature = cas,
        num.bugs = "auto",
        metadata.factor = 5,
        column.stratification.order =  c("Subgingival_plaque","Supragingival_plaque","Buccal_mucosa","Saliva","Tongue_dorsum","Throat","Hard_palate","Keratinized_gingiva","Palatine_Tonsils","Stool","Anterior_nares","L_Retroauricular_crease","R_Retroauricular_crease","R_Antecubital_fossa","Mid_vagina","Posterior_fornix","Vaginal_introitus"),
        num.bugs.explained.fraction = 0.35,
        order.by = "custom",
        custom.order = custom.order,
        last.plot.colors = plot.colors
      )

    p <-
      makeHumann2Barplot(
        dat,
        last.plot.colors = plot.colors,
        hide.legend = F,
        fixed.floor = -1,
        sample.threshold = sample.threshold,
        fixed.ymax = 3,
        scale = "proportional-log",
        space = "fixed",
        hide.strata.legend = F
        )
  })
}

  pdf("figure6_with_legend.pdf", height = 10, width = 9)
print(multiplot(plotlist = cas_plots, cols = 2))
dev.off()

philippmuench/PMtools documentation built on Dec. 27, 2019, 8:08 a.m.