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neurogenomics · Apr 25, 2024 · 1e529e0 · 1e529e0
2 parents efb099e + 68733fd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: EpiCompare
 Title: Comparison, Benchmarking & QC of Epigenomic Datasets
-Version: 1.7.3
+Version: 1.7.5
 Authors@R: c(
     person(given = "Sera", family = "Choi", 
         email = "serachoi1230@gmail.com", 
@@ -51,7 +51,7 @@ Imports:
     GenomicRanges,
     IRanges,
     GenomeInfoDb,
-    ggplot2,
+    ggplot2 (>= 3.5.0),
     htmltools,
     methods,
     plotly, 
@@ -98,4 +98,4 @@ biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: FALSE
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/R/overlap_upset_plot.R b/R/overlap_upset_plot.R
@@ -75,9 +75,9 @@ overlap_upset_plot <- function(peaklist,
       text_mapping=ggplot2::aes(label=!!ComplexUpset::upset_text_percentage())
     )
   )
-  plt <- ComplexUpset::upset(data = overlap_df, 
-                             intersect = peaklist_names, 
-                             base_annotations = base_annotations)   
+  plt <- ComplexUpset::upset(data = overlap_df,
+                             intersect = peaklist_names,
+                             base_annotations = base_annotations)
   # upset_plot <- UpSetR::upset(data = overlap_df, 
   #                             order.by = "freq",
   #                             mb.ratio = c(0.60, 0.40),

diff --git a/R/plot_chromHMM.R b/R/plot_chromHMM.R
@@ -102,7 +102,7 @@ plot_chromHMM <- function(peaklist,
                                     fill = value)) +
     ggplot2::ylab("") +
     ggplot2::xlab("") +
-    ggplot2::scale_fill_viridis_b() +
+    ggplot2::scale_fill_viridis_c() +
     ggplot2::theme_minimal() +
     ggplot2::theme(axis.text = ggplot2::element_text(size = 11)) +
     ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 315,

diff --git a/inst/markdown/EpiCompare.Rmd b/inst/markdown/EpiCompare.Rmd
@@ -346,8 +346,8 @@ upset_plot <- NULL
 if(isTRUE(params$upset_plot)){
   upset_plot <- overlap_upset_plot(peaklist = peaklist_tidy)
   download_button(object = upset_plot,
-                  filename = "upset_plot", 
-                  add_download_button = params$add_download_button) 
+                  filename = "upset_plot",
+                  add_download_button = params$add_download_button)
   save_output(save_output = params$save_output,
               file = upset_plot,
               file_type = "image",
@@ -527,23 +527,23 @@ ChromHMM annotation of individual samples.
 ```{r plot_chromHMM1, fig.width=9, fig.height=fig_height} 
 samples_chromHMM <- NULL
 if(isTRUE(params$chromHMM_plot)){
-  # Get ChromHMM annotation file 
+  # Get ChromHMM annotation file
   chromHMM_list <- get_chromHMM_annotation(cell_line = params$chromHMM_annotation)
   # Plot chromHMM
-  samples_chromHMM <- plot_chromHMM(peaklist = peaklist_tidy, 
-                                    chromHMM_annotation = chromHMM_list, 
+  samples_chromHMM <- plot_chromHMM(peaklist = peaklist_tidy,
+                                    chromHMM_annotation = chromHMM_list,
                                     genome_build = output_build,
                                     interact = params$interact)
   download_button(object = samples_chromHMM,
                   filename = "samples_ChromHMM",
                   self_contained = params$interact,
-                  add_download_button = params$add_download_button) 
+                  add_download_button = params$add_download_button)
   save_output(save_output = params$save_output,
               file = samples_chromHMM,
               file_type = "ggplot",
               filename = "samples_ChromHMM",
               outpath = outfile_dir,
-              interactive = params$interact)  
+              interactive = params$interact)
 }
 samples_chromHMM
 remove(samples_chromHMM)

diff --git a/tests/test.Rmd b/tests/test.Rmd
@@ -0,0 +1,62 @@
+---
+title: "`r EpiCompare::report_header()`"
+date: "`r format(Sys.Date(), '%b-%d-%Y')`"
+output: 
+  html_document: 
+    toc: yes
+    toc_float: yes
+    code_folding: hide 
+    number_sections: true
+    css: custom.css
+params:
+  peakfiles: 
+    value: NULL
+  output_dir: 
+    value: NULL
+  genome_build:
+    value: NULL
+  genome_build_output:
+    value: "hg19"
+  blacklist: 
+    value: NULL
+  picard_files:
+    value : NULL
+  reference: 
+    value: NULL
+  upset_plot:
+    value: FALSE
+  stat_plot:
+    value: FALSE
+  chromHMM_plot:
+    value: FALSE
+  chromHMM_annotation:
+    value: "K562"
+  chipseeker_plot:
+    value: FALSE
+  enrichment_plot:
+    value: FALSE
+  tss_plot:
+    value: FALSE
+  tss_distance:
+    value: c(-3000,3000)
+  precision_recall_plot:
+    value: FALSE
+  n_threshold:
+    value: 15
+  corr_plot:
+    value: FALSE  
+  bin_size:
+    value: 5000      
+  interact:
+    value: TRUE
+  add_download_button:
+    value: TRUE
+  save_output:
+    value: FALSE
+  workers:
+    value: 1
+  error:
+    value: FALSE
+  debug:
+    value: FALSE
+---
diff --git a/tests/test.html b/tests/test.html
diff --git a/tests/testthat/test-EpiCompare.R b/tests/testthat/test-EpiCompare.R
@@ -62,3 +62,5 @@ testthat::test_that("EpiCompare works",{
   # testthat::expect_true(is.element("fragment_info.csv", files))
   # testthat::expect_true(is.element("processed_peakfiles_hg19", files))
 })
+
+