Heat tree for QIIME OTU tables

[Richard Rodrigues]

Hi Zach

Based on your replies to previous similar question(s), I was able to parse the OTU table and view a heat tree. I was wondering if you can help me how to use the "sum" column from the OTU table. Secondly, I was wondering if we can use (average) relativised abundances for the heat tree.

library(metacoder)
file = 'cc_count_sum_abund.txt'
outfile = 'genus-v1.pdf'

df = read.table(file, header=T, check.names=F, sep='\t')
head(df)
colnames(df)[ncol(df)] = 'class'
colnames(df)[1] = "obs_info"

data = parse_taxonomy_table(df, taxon_col = c("class" = -1), other_col_type = "obs_info", class_sep = ";")

pdf(outfile)
set.seed(1)
filter_taxa(data, n_supertaxa < 6) %>%  
  heat_tree(node_size = n_obs, node_color_range = c("white", "#DFDFDF", "gray75", "#c6e1f6", "#6db9f2"), node_label = name, node_color = n_obs)
dev.off()

Thanks.

-Rich

[Zachary Foster]

Hello Rich,

Sorry for the delay! The holidays slowed me down and I have a back log of emails to get to. Check out the attached and let me know if you have questions.

Best,

-Zach

[Richard Rodrigues]

No worries, this is fantastic!

Btw, I use following to save the plots

pdf(name.pdf)
heat_tree cmd
dev.off()

 but it creates a two page pdf, first page is blank and the image shows on the second. Is this something that is specific to me (the method I try to save)?

Thanks.

-Rich

[Zachary Foster]

Hi Rich,

Did you try the "output_file" option in "heat_tree"? That can save a PDF, but it will be the size of the plot, not a page size.

Best,

Zach

[Richard Rodrigues]

Not yet, I'll try it. Thanks.