heatmap about microbiomeutilities HOT 8 CLOSED

Thanks for the query. Which function did you use ? and I don't see the attached heat map 😉

from microbiomeutilities.

thanks, I use the plot_taxa_heatmap. sorry, i forgot to attach the heat map. I followed the same tutorial.

from microbiomeutilities.

It is not possible at the moment. I will try to re-write this function.
For the other part, you can make a phyloseq object at the level you want and provide it as input.
Try ps.family <- aggregate_taxa(ps0, "Family") to get family level data and use it as input for plotting.

Edit: Does your species column in tax_table(ps) have only species name? If yes you need to merge genus and species to get genus.species.

from microbiomeutilities.

thanks for your answer. I tried your suggested solution and I got the desired results.
the code I used as below.
I am curious about the use of gsub as in my taxa labeling I don't have the d__denovo, is it possible to omit it? also the label in the plot show two time the family name.
for species, I have only the species names. how to merge genus and species column?
sorry for the trouble.
library(microbiomeutilities)
library(microbiome)
library(knitr)
library(tibble)
library(dplyr)
library(pheatmap)
library(RColorBrewer)
ps = import_biom("RiceOTUN150kp1cleanaddOther.biom", treefilename="RiceOTUreduced.tre", parseFunction= parse_taxonomy_greengenes)
ps
ps.family <- aggregate_taxa(ps, "Family")
taxa_names(ps.family) <- gsub("d__denovo", "OTU:", taxa_names(ps.family))
grad_ab <- colorRampPalette(c("#faf3dd","#f7d486" ,"#5e6472"))
grad_ab_pal <- grad_ab(10)
gray_grad <- colorRampPalette(c("white", "steelblue"))
gray_grad_cols <- gray_grad(10)

meta_colors <- list(c("Odae" = "#FFC857",
"Ilpoom" = "#05B083"),
c("Hull" = "steelblue",
"BrownRice" = "grey50",
"WhiteRice"="brown3"),
gray_grad_cols)
names(meta_colors) <- c("cultivar", "Tissue")
p <- plot_taxa_heatmap(ps,
subset.top = 25,
VariableA = c("cultivar","Tissue"),
heatcolors = grad_ab_pal, #rev(brewer.pal(6, "RdPu")),
transformation = "log10",
cluster_rows = T,
cluster_cols = F,
show_colnames = F,
annotation_colors=meta_colors)

from microbiomeutilities.

Good. I also removed the prevalence option from the plot in latest v1.00.13. For gsub check this primer on the parent microbiome R package website. The duplicate labelling is because you add it with gsub. You can skip it. For merging genus+species, I am not sure how your species column looks like and therefore cannot provide a direct solution. You should be able to find a solution online. If you do, please post it here for others :)

from microbiomeutilities.

thanks a lot. for the gsub, I omitted but still give double name. the taxa table is as follow (kable(head(tax_table(ps))[3:6])):
.

from microbiomeutilities.

Try this to merge genus.species

library(tibble)
library(dplyr)
tax_tb <- as(tax_table(ps),"matrix") %>% 
  as.data.frame() %>% 
  rownames_to_column("ASV") %>% 
  mutate(Genus.Species = ifelse(!is.na(Species), paste0(Genus, ".", Species), Species)) %>% 
  select(-Species)   %>% 
rename(Species = Genus.Species)

#tax_tb[1:30, 5:9]
rownames(tax_tb) <- tax_tb$ASV
tax_tb <- tax_tb[,-1]

tax_table(ps) <- tax_table(as.matrix(tax_tb))

from microbiomeutilities.

thank you a lot for your help. one question if possible, the order in heatmap is fixed based on what? if I want the most abundant to be on the first row, should i modify the function?

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