library(SummarizedExperiment)
+#> Loading required package: MatrixGenerics
+#> Loading required package: matrixStats
+#>
+#> Attaching package: ‘MatrixGenerics’
+#> The following objects are masked from ‘package:matrixStats’:
+#>
+#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
+#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
+#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
+#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
+#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
+#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
+#> colWeightedMeans, colWeightedMedians, colWeightedSds,
+#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
+#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
+#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
+#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
+#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
+#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
+#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
+#> rowWeightedSds, rowWeightedVars
+#> Loading required package: GenomicRanges
+#> Loading required package: stats4
+#> Loading required package: BiocGenerics
+#>
+#> Attaching package: ‘BiocGenerics’
+#> The following objects are masked from ‘package:stats’:
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+#> IQR, mad, sd, var, xtabs
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+#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
+#> as.data.frame, basename, cbind, colnames, dirname, do.call,
+#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
+#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
+#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
+#> tapply, union, unique, unsplit, which.max, which.min
+#> Loading required package: S4Vectors
+#>
+#> Attaching package: ‘S4Vectors’
+#> The following object is masked from ‘package:utils’:
+#>
+#> findMatches
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+#> I, expand.grid, unname
+#> Loading required package: IRanges
+#> Loading required package: GenomeInfoDb
+#> Loading required package: Biobase
+#> Welcome to Bioconductor
+#>
+#> Vignettes contain introductory material; view with
+#> 'browseVignettes()'. To cite Bioconductor, see
+#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
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+#> Attaching package: ‘Biobase’
+#> The following object is masked from ‘package:MatrixGenerics’:
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+#> rowMedians
+#> The following objects are masked from ‘package:matrixStats’:
+#>
+#> anyMissing, rowMedians
+# Generate some artificial data that shows a difference in Zak_RISK_16
+mat_testdata <- rbind(matrix(c(rnorm(80), rnorm(80) + 5), 16, 10,
+ dimnames = list(paste0("Taxon", seq_len(16)),
+ paste0("sample", seq_len(10)))),
+ matrix(rnorm(1000), 100, 10,
+ dimnames = list(paste0("Taxon0", seq_len(100)),
+ paste0("sample", seq_len(10)))))
+cov_mat <- data.frame(sample = c(rep("down", 5), rep("up", 5))) |>
+ magrittr::set_rownames(paste0("sample", seq_len(10)))
+
+# Example using custom colors for the annotation information
+color2 <- stats::setNames(c("purple", "black"), c("down", "up"))
+color.list <- list("sample" = color2)
+
+plot_heatmap(
+ inputData = mat_testdata,
+ annotationData = cov_mat,
+ name = "Data",
+ plot_title = "Example",
+ plottingColNames = NULL,
+ annotationColNames = NULL,
+ colList = color.list,
+ scale = FALSE,
+ showColumnNames = TRUE,
+ showRowNames = FALSE,
+ colorSets = c("Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Accent", "Dark2",
+ "Paired"),
+ choose_color = c("blue", "gray95", "red"),
+ split_heatmap = "none",
+ column_order = NULL
+)
+
+
+