## ----echo = FALSE------------------------------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.align = "center" ) ## ----echo = FALSE------------------------------------------------------------- suppressPackageStartupMessages(library(InteractiveComplexHeatmap)) ## ----eval = FALSE------------------------------------------------------------- # library(ComplexHeatmap) # library(InteractiveComplexHeatmap) # m = matrix(rnorm(100*100), nrow = 100) # ht = Heatmap(m) # ht = draw(ht) # not necessary, but recommended # # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # # the following code is runable # library(cola) # cola is from Bioconductor # data(golub_cola) # get_signatures(golub_cola["ATC:skmeans"], k = 2) # this makes the heatmap # htShiny() ## ----eval = FALSE------------------------------------------------------------- # htShiny(ht, output_ui_float = TRUE) ## ----eval = FALSE------------------------------------------------------------- # htShiny(ht, compact = TRUE) ## ----eval = FALSE------------------------------------------------------------- # set.seed(123) # mat1 = matrix(rnorm(100), 10) # rownames(mat1) = colnames(mat1) = paste0("a", 1:10) # mat2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10) # rownames(mat2) = colnames(mat2) = paste0("b", 1:10) # # ht_list = Heatmap(mat1, name = "mat_a", row_km = 2, column_km = 2) + # Heatmap(mat2, name = "mat_b") # htShiny(ht_list) ## ----eval = FALSE------------------------------------------------------------- # ht_list = Heatmap(mat1, name = "mat_a", row_km = 2, column_km = 2) %v% # Heatmap(mat2, name = "mat_b") # htShiny(ht_list) ## ----eval = FALSE------------------------------------------------------------- # ht = densityHeatmap(...) # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # ht = oncoPrint(...) # htShiny(ht) # # ht = oncoPrint(...) + Heatmap(...) + rowAnnotation(...) # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # cm = make_comb_mat(...) # ht = UpSet(cm, ...) # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # mat = normalizeToMatrix(...) # ht = EnrichedHeatmap(mat, ...) # htShiny(ht) # # ht = EnrichedHeatmap(mat, ...) + EnrichedHeatmap(...) + Heatmap(...) # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # ht = pheatmap(...) # ComplexHeatmap::pheatmap should overwrite pheatmap::pheatmap # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # ht = ComplexHeatmap:::heatmap(...) # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # ht = ComplexHeatmap:::heatmap.2(...) # htShiny(ht) ## ----eval = FALSE------------------------------------------------------------- # library(tidyverse) # library(tidyHeatmap) # mtcars_tidy <- # mtcars %>% # as_tibble(rownames="Car name") %>% # mutate_at(vars(-`Car name`, -hp, -vs), scale) %>% # pivot_longer(cols = -c(`Car name`, hp, vs), names_to = "Property", values_to = "Value") # # mtcars_heatmap <- # mtcars_tidy %>% # heatmap(`Car name`, Property, Value ) %>% # add_tile(hp) # # htShiny(mtcars_heatmap) ## ----eval = FALSE------------------------------------------------------------- # ComplexHeatmap::pheatmap(...) # htShiny() # # oncoPrint(...) # htShiny() ## ----------------------------------------------------------------------------- htShinyExample() ## ----eval = FALSE------------------------------------------------------------- # htShinyExample(1.4) ## ----------------------------------------------------------------------------- sessionInfo()