Initial commit

NAMESPACE

@@ -63,6 +63,7 @@ export(adjust_flip)
 export(adjust_fontsize)
 export(adjust_labels)
 export(adjust_legend)
+export(adjust_padding)
 export(adjust_size)
 export(adjust_x_axis)
 export(adjust_y_axis)

R/adjust.R

@@ -326,6 +326,20 @@ adjust_legend <- function(gg, title = ggplot2::waiver(), position = "right") {
     ggplot2::theme(legend.position = position)
 }
 
+#' Adjust padding
+#' @param gg bla
+#' @param top bla
+#' @param right bla
+#' @param bottom bla
+#' @param left bla
+#' @param force_y_continuous bla
+#' @export
+adjust_padding <- function(gg, top = NULL, right = NULL, bottom = NULL, left = NULL, force_y_continuous = FALSE) {
+  gg %>%
+    adjust_x_axis(padding_left = left, padding_right = right) %>%
+    adjust_y_axis(padding_bottom = bottom, padding_top = top, force_y_continuous = force_y_continuous)
+}
+
 #' Flip plot
 #' @param gg bla
 #' @param ... bla

R/data.R

@@ -12,11 +12,11 @@
 #' `tidyplots` package
 "gene_statistics"
 
-#' Disease course data
+#' Time course data
 #' @format A data frame with 800 rows and 9 variables.
 #' @source
 #' `tidyplots` package
-"disease_course"
+"time_course"
 
 #' Energy data
 #' @format A data frame with 242 rows and 4 variables.

R/todo.R

@@ -1,12 +1,4 @@
 
-# heatmap have no color legend
-
-# adjust_padding(tlbr)
-
-# data set "de_analysis" for volcano plots
-
-# data set "disease_course" for plotting
-
 # work on check_pipeline()
 # enforce "sequence of funs", with warnings and errors
 

_pkgdown.yml

@@ -68,6 +68,7 @@ reference:
   - starts_with("adjust_size")
   - starts_with("adjust_fontsize")
   - starts_with("adjust_legend")
+  - starts_with("adjust_padding")
   - starts_with("adjust_flip")
   - starts_with("adjust_annotation")
 - title: Themes
@@ -99,4 +100,4 @@ reference:
   - starts_with("study")
   - gene_expression
   - gene_statistics
-  - disease_course
+  - time_course

data-raw/gene_expression.R

@@ -5,3 +5,13 @@ library(tidyverse)
 gene_expression <- read_csv(file = "data-raw/gene_expression.csv")
 
 usethis::use_data(gene_expression, overwrite = TRUE)
+
+library(tidyplots)
+library(tidyverse)
+
+gene_expression %>%
+  tidyplot(sample, external_gene_name, color = expression, width = 100) %>%
+  add_heatmap(scale = "row") %>%
+  adjust_labels(var = external_gene_name, sort_by = -padj) %>%
+  adjust_labels(var = direction, reverse = TRUE)+
+  facet_wrap(vars(direction), scales = "free")

data-raw/disease_course.R → data-raw/time_course.R

@@ -1,29 +1,30 @@
-## code to prepare `disease_course` dataset goes here
+## code to prepare `time_course` dataset goes here
 
 library(tidyverse)
 
-disease_course <-
-  read_tsv("data-raw/tidy_disease_course.txt")
+time_course <-
+  read_tsv("data-raw/time_course.txt")
 
-usethis::use_data(disease_course, overwrite = TRUE)
+usethis::use_data(time_course, overwrite = TRUE)
 
-library(tidyplots)
-
-disease_course %>%
+time_course %>%
   tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>%
   add_mean_line() %>%
   add_mean_dot() %>%
   add_error_ribbon()
 
-disease_course %>%
+library(tidyverse)
+
+time_course %>%
   tidyplot(x = day, y = subject, color = score, height = 80) %>%
   add_heatmap(rotate_labels = FALSE) +
   facet_grid(vars(treatment), scales = "free")
 
-disease_course %>%
+time_course %>%
   tidyplot(x = day, y = subject, color = score, height = 80) %>%
   add_heatmap(rotate_labels = FALSE) %>%
   adjust_colors(new_colors = rev(RColorBrewer::brewer.pal(n = 7, name = "RdYlBu")),
                 as_palette = TRUE,
                 na.value = "#DDDDDD") +
   facet_grid(vars(treatment), scales = "free")
+