PMtools

Miscellaneous helper functions mostly for comparative genomics, metagenomics and package development from P. Münch at LMU Munich & Helmholtz Centre for Infection Research.

install.packages("devtools")
devtools::install_github("philippmuench/PMtools")

usage

HUMAnN2 tools

generation of barplots

# load example datasets
data(humann2_table)
data(hmp1_2_metadata)
data(hmp1_2_metaphlan)

Command to generate a figure of a single feature. Set num.bugs = "auto" to automatically adjust the number of bugs needed to show 25% of RA

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

# generate the data used for plotting
dat <-
  humann2Barplot(
    humann2_table,
    metadata = hmp1_2_metadata,
    feature = "Cas2",
    num.bugs = "auto",
    order.by = "custom",
    custom.order = custom.order
  )
  
# generate the plot
p <-
  makeHumann2Barplot(
    dat,
    NULL,
    hide.legend = F,
    scale = "pseudolog",
    space = "fixed"
  )

# show figure
print(p$gplot)

re-use colors

# generate the data used for plotting
dat_plot1 <-
  humann2Barplot(
    humann2_table,
    metadata = hmp1_2_metadata,
    feature = "Cas1",
    num.bugs = "auto",
    order.by = "custom",
    custom.order = custom.order
  )
  
# generate the data used for plotting
dat_plot2 <-
  humann2Barplot(
    humann2_table,
    metadata = hmp1_2_metadata,
    feature = "Cas2",
    num.bugs = "auto",
    order.by = "custom",
    custom.order = custom.order
  )
  
# generate the plot
p1 <-
  makeHumann2Barplot(
    dat_plot1,
    NULL,
    hide.legend = F,
    scale = "pseudolog",
    space = "fixed"
  )

# generate the plot
p2 <-
  makeHumann2Barplot(
    dat_plot2,
    p1$colors,
    hide.legend = F,
    scale = "pseudolog",
    space = "fixed"
  )
# same taxa now have the same color
print(p1$gplot)
print(p2$gplot)

you can also plot multiple features into one figure

cas_plots <- vector('list', 10)
plot.colors <- NULL
for (cas in paste0("Cas", 1:10)) {
  cas_plots[[cas]]  <- local({
    dat <-
      humann2Barplot(
        humann2_table,
        metadata = hmp1_2_metadata,
        feature = cas,
        num.bugs = "auto",
        num.bugs.explained.fraction = 0.35,
        order.by = "custom",
        custom.order = custom.order
      )
    p <-
      makeHumann2Barplot(
        dat,
        plot.colors,
        hide.legend = F,
        scale = "pseudolog",
        space = "fixed"
        )
    plot.colors <<- rbind(plot.colors, p$colors)
    write.table(p$colors, file="log.txt", append=T, sep ="\t", row.names=F,
    col.names=F, quote=F)
    print(p$gplot)
  })
}

# you can plot these together
pdf("all_cas.pdf", width = 6, height = 7)
print(multiplot(plotlist = cas_plots, cols = 2))
dev.off()

# or access each plot individually 
print(cas_plots[["Cas1"]])
# and the data underlying the plot
cas_plots[["Cas1"]]$dat

License and copyright

Copyright 2019 Philipp Münch

Source code to PMtools is made available under the terms of the GNU Affero General Public License (AGPL). PMtools is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.