library(ggplot2)
library(RColorBrewer)
library(pheatmap)

## Warning: package 'pheatmap' was built under R version 4.4.1

library(viridis)

## Loading required package: viridisLite

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(plotly)

## Warning: package 'plotly' was built under R version 4.4.3

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

# setwd("/Users/veronicapagowski/Desktop/HeatmapTest") # change to your directory
setwd("/Users/mala/CZID_Patiria_Samples_Aug2025")

Heatmap: Plot the unfiltered heatmap

Heatmap: Plot the filtered heatmap (different format)

## taxons.csv read, but no taxa intersect with heat_mat2 rownames; using full heat_mat2.

## HC matrix has no finite/non-zero values; skipping HC heatmap.