rmflight · July 24, 2020 00:26 · Mar 26, 2020 · Oct 1, 2019 · Oct 1, 2019 · Oct 31, 2018
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -1,3 +1,21 @@
+# ComplexHeatmap
+
+## Modify the font sizes in the heatmap
+
+If you want to get the font sizes right for a plot, you will need to play with these font sizes
+
+```r
+# add the following, add col* if you want to modify both
+row_names_gp = gpar(fontsize = 24, fontfamily = "FreeMono")
+```
+
+## Saving a PNG
+
+```r
+Cairo("filename", width = 2600, height = 6210, dpi = 300, bg = "#FFFFFF", fontfamily = "FreeMono")
+Heatmap(heatmap, colormap, "Expression", cluster_rows = FALSE, cluster_columns = FALSE, row_names_gp = gpar(fontsize = 24, fontfamily = "FreeMono"), column_names_gp = gpar(fontsize = 30))
+dev.off()
+```
 # ggplot2
 
 ## Rotate axis tick labels 90 degrees

diff --git a/code_counting.md b/code_counting.md
@@ -1 +1,13 @@
-If you want to know how many lines of code are in 
+If you want to know how many lines of code are in an Rmd file:
+
+```
+rmarkdown::render("file.Rmd", output_format = "md_document")
+
+cat file.md | grep -c '^ \{4\}'
+```
+
+And then how many lines of code in .R files:
+
+```
+wc --lines file.R
+```
diff --git a/code_counting.md b/code_counting.md
@@ -0,0 +1 @@
+If you want to know how many lines of code are in 
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -104,6 +104,8 @@ correctly_round_numbers <- function(number_of_things, fraction){
 
 ## Anonymize Things While Retaining Order
 
+Courtesy of [David Robinson](https://twitter.com/drob/status/1057681171105173504)
+
 ```
 as.integer(fct_inorder(x))
 ```
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -101,3 +101,9 @@ correctly_round_numbers <- function(number_of_things, fraction){
   floor_value
 }
 ```
+
+## Anonymize Things While Retaining Order
+
+```
+as.integer(fct_inorder(x))
+```
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -87,3 +87,17 @@ ggplot(rf_sep, aes(x = dim1, y = dim2, color = class)) + geom_point()
 * BioCann: https://bioconductor.org/packages/3.4/data/annotation
 * BioCexp: https://bioconductor.org/packages/3.4/data/experiment
 * BioCextra: https://bioconductor.org/packages/3.4/extra
+
+## Easily switch between fraction and number of things
+
+```
+correctly_round_numbers <- function(number_of_things, fraction){
+  assertthat::assert_that(number_of_things > 0)
+  if (fraction < 1) {
+    floor_value <- floor(number_of_things * fraction)
+  } else {
+    floor_value <- number_of_things
+  }
+  floor_value
+}
+```
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -28,6 +28,22 @@ ggsave("filename.svg", plot_to_save)
 system("inkscape -z -d 300 -e outfile.png infile.svg")
 ```
 
+## Include cowplot in package deps
+
+If we want to use the cowplot theme, but keep from generating warnings, etc in R CMD check of when `loading` the package, then we should structure things like so:
+
+```r
+#' @import ggplot2
+
+theme_set(cowplot::theme_cowplot())
+```
+
+And in DESCRIPTION:
+
+```
+imports: ggplot2, cowplot
+```
+
 # Inkscape
 
 ## Add a bullet

diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -28,6 +28,21 @@ ggsave("filename.svg", plot_to_save)
 system("inkscape -z -d 300 -e outfile.png infile.svg")
 ```
 
+# Inkscape
+
+## Add a bullet
+
+```
+ctrl+u, 2022, enter
+```
+
+## Flow Text Around an Object
+
+* Draw a path around the object using whatever tool you want
+* Select the previous written text's box
+* Select the path object
+* Text -> Flow into Frame
+
 # Random Forest
 
 ## Separability plot

diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -12,6 +12,22 @@
 + theme(legend.position="none")
 ```
 
+## Make COWPLOT fontsize a bit bigger
+
+```r
+mod_theme <- theme_cowplot(font_size = 16)
+theme_set(mod_theme)
+```
+
+## Make PNG of high-density SVGs
+
+SVG is great for posters, can resize at will. But if there are a lot of points, then we really want PNG. This workflow we export the point figure to SVG at the set size, and then convert to PNG using InkScape at the command line.
+
+```r
+ggsave("filename.svg", plot_to_save)
+system("inkscape -z -d 300 -e outfile.png infile.svg")
+```
+
 # Random Forest
 
 ## Separability plot

diff --git a/testing_stuff.md b/testing_stuff.md
@@ -0,0 +1,31 @@
+## working with temp temp directories
+
+```r
+create_in_temp <- function(dir_loc, create_it = TRUE) {
+  temp_path <- tempfile(pattern = paste0("copyfiles-test-", dir_loc))
+  if (create_it) {
+    dir.create(temp_path)
+  }
+  temp_path
+}
+erase <- function(path) unlink(path, recursive = TRUE)
+```
+
+## skipping tests conditionally
+
+- in ci have `export skip_variable=TRUE`
+
+```r
+skip_variable <- as.logical(Sys.getenv("skip_variable"))
+if (is.na(skip_variable)) {
+  skip_variable <- FALSE
+}
+
+test_that("test we want to skip conditionally", {
+  skip_if_not(skip_variable)
+  expect_true(test condition)
+})
+
+test_that("other tests", {
+
+})
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -6,6 +6,12 @@
 + theme(axis.text.x = element_text(angle = 90))
 ```
 
+## Remove the legend
+
+```r
++ theme(legend.position="none")
+```
+
 # Random Forest
 
 ## Separability plot

diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -25,4 +25,12 @@ names(rf_sep) <- c("dim1", "dim2")
 rf_sep$class <- factor_of_classes
 
 ggplot(rf_sep, aes(x = dim1, y = dim2, color = class)) + geom_point()
-```
+```
+
+## Install Specific Bioconductor Package Versions
+
+* modify the `repos` argument based on `BiocInstaller::biocinstallRepos`:
+* BioCsoft: https://bioconductor.org/packages/3.4/bioc
+* BioCann: https://bioconductor.org/packages/3.4/data/annotation
+* BioCexp: https://bioconductor.org/packages/3.4/data/experiment
+* BioCextra: https://bioconductor.org/packages/3.4/extra
diff --git a/graphing_errors.md b/graphing_errors.md
@@ -1,7 +0,0 @@
-## Get an error about X11 Missing font
-
-`X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 12 could not be loaded`
-
-The solution is:
-
-`X11.options(type = "cairo")`

diff --git a/graphing_issues.md b/graphing_issues.md
@@ -0,0 +1,21 @@
+## Get an error about X11 Missing font
+
+`X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 12 could not be loaded`
+
+The solution is:
+
+`X11.options(type = "cairo")`
+
+## Want to use a particular font in a graphic
+
+For example, to add a Monospaced font to a graphic instead of a proportional font:
+
+```
+library(showtext)
+font.add("FreeMono", "FreeMono.ttf")
+showtext.auto()
+
+Cairo("graphic.png", width = 2600, height = 3600, dpi = 300, bg = "#FFFFFF", fontfamily = "FreeMono")
+plot(..., gpar(fontsize = 24, fontfamily = "FreeMono"))
+dev.off()
+```
diff --git a/install_problems.md b/install_problems.md
@@ -4,4 +4,14 @@
 R CMD javareconf -e
 ```
 
-Restart R / RStudio (i.e. complete shutdown and restart)
+Restart R / RStudio (i.e. complete shutdown and restart)
+
+# rJava, no jni.h
+
+If you've confirmed that jni.h can be found, and that
+
+`R CMD javareconf -n`
+
+still shows an error, and it seems to be mainly due to using the incorrect directory for JAVA, one solution may be to make a link from the directory `R` wants to use, to the actual one.
+
+`sudo ln /usr/lib/jvm/right_java_dir /usr/lib/jvm/wrong_java_dir`
diff --git a/graphing_errors.md b/graphing_errors.md
@@ -0,0 +1,7 @@
+## Get an error about X11 Missing font
+
+`X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 12 could not be loaded`
+
+The solution is:
+
+`X11.options(type = "cairo")`
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -52,4 +52,22 @@ xtable::caption(tmp_table) <- "caption text"
 xtable::align(out_table) <- "llp{2in}ll" # assuming 4 column table, second column would only take up 2 inches of space
 print(out_table, comment = FALSE, floating = FALSE, tabular.environment = "longtable") # important at end, to make sure that the environment is correct, because otherwise the tables won't display right, believe me
 
+```
+
+## Setting Parameters
+
+```r
+parameters = read_delim(
+
+'Parameter     | Value | Units 
+#--------------|-------|-------
+ herd_size     | 20.00 | camels
+ max_age       | 25.00 | years
+ fertile_age   |  5.00 | years ',
+
+ delim = '|', trim_ws = TRUE, comment = "#')
+ 
+input = structure(as.list(parameters$Value),
+                  names = parameters$Parameter)
+kable(parameters, align = c('l', 'r', 'l'), caption = 'Model Parameters')
 ```
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -13,10 +13,9 @@ output:
 ## Knitr chunk setup
 
 ```
-```{r setup, echo=FALSE}
+{r setup, echo=FALSE}
 knitr::opts_chunk$set(cache = TRUE, warning = FALSE, message = FALSE)
 ```
-```
 
 ## Data Checking
 

diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -10,6 +10,14 @@ output:
 ---
 ```
 
+## Knitr chunk setup
+
+```
+```{r setup, echo=FALSE}
+knitr::opts_chunk$set(cache = TRUE, warning = FALSE, message = FALSE)
+```
+```
+
 ## Data Checking
 
 ```{r data_checking}

diff --git a/using_reporters.md b/using_reporters.md
@@ -0,0 +1,11 @@
+```r
+library(ReporteRs)
+doc <- pptx()
+
+p <- ggplot() ....
+
+doc <- addSlide(doc, slide.layout = "Content with Caption")
+doc <- addPlot(doc = doc, fun = print, x = p, vector.graphic = TRUE)
+
+writeDoc(doc = doc, file = "file.pptx")
+```
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -32,13 +32,17 @@ knitr::kable(pkg_info$packages)
 ---
 header-includes:
   - \usepackage{longtable} # allows use of tables spanning pages
+  - \usepackage{caption} # used if you need to define your own captions
+  - \captionsetup{labelformat = empty} # for empty captions
 output: pdf_document
 classoption: landscape # turns output to landscape
 ---
 ```
 
 ```{r table_output}
 out_table <- xtable::xtable(df, type = "latex")
+xtable::caption(tmp_table) <- "caption text"
 xtable::align(out_table) <- "llp{2in}ll" # assuming 4 column table, second column would only take up 2 inches of space
 print(out_table, comment = FALSE, floating = FALSE, tabular.environment = "longtable") # important at end, to make sure that the environment is correct, because otherwise the tables won't display right, believe me
+
 ```
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -28,12 +28,14 @@ knitr::kable(pkg_info$packages)
 
 ## Wide Format PDF Tables in RMarkdown
 
+```
 ---
 header-includes:
   - \usepackage{longtable} # allows use of tables spanning pages
 output: pdf_document
 classoption: landscape # turns output to landscape
 ---
+```
 
 ```{r table_output}
 out_table <- xtable::xtable(df, type = "latex")

diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -25,3 +25,18 @@ pkg_info <- devtools::session_info()
 pkg_info$platform
 knitr::kable(pkg_info$packages)
 ```
+
+## Wide Format PDF Tables in RMarkdown
+
+---
+header-includes:
+  - \usepackage{longtable} # allows use of tables spanning pages
+output: pdf_document
+classoption: landscape # turns output to landscape
+---
+
+```{r table_output}
+out_table <- xtable::xtable(df, type = "latex")
+xtable::align(out_table) <- "llp{2in}ll" # assuming 4 column table, second column would only take up 2 inches of space
+print(out_table, comment = FALSE, floating = FALSE, tabular.environment = "longtable") # important at end, to make sure that the environment is correct, because otherwise the tables won't display right, believe me
+```
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -10,13 +10,18 @@ output:
 ---
 ```
 
+## Data Checking
 
+```{r data_checking}
+library(assertthat)
+library(assertr)
+```
 
 
-## Software Used
+## Packages Used
 
-```{r software_used}
-dev_info <- devtools::session_info()
-dev_info$platform
-knitr::kable(dev_info$packages)
+```{r packages_used, echo = FALSE}
+pkg_info <- devtools::session_info()
+pkg_info$platform
+knitr::kable(pkg_info$packages)
 ```
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -1,5 +1,3 @@
-# Vignette title
-
 ```
 ---
 title: "a good title"
@@ -10,4 +8,15 @@ output:
   pdf_document: 
     toc: yes
 ---
-```
+```
+
+
+
+
+## Software Used
+
+```{r software_used}
+dev_info <- devtools::session_info()
+dev_info$platform
+knitr::kable(dev_info$packages)
+```
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -24,5 +24,5 @@ names(rf_sep) <- c("dim1", "dim2")
 # add your class information so can see how classes behave relative to one another using coloring (or shape, etc)
 rf_sep$class <- factor_of_classes
 
-ggplot(rf_sep, aes(x = dim1, y = dim2, color = class) + geom_point()
+ggplot(rf_sep, aes(x = dim1, y = dim2, color = class)) + geom_point()
 ```
diff --git a/install_problems.md b/install_problems.md
@@ -0,0 +1,7 @@
+# rJava: can't load .so object
+
+```
+R CMD javareconf -e
+```
+
+Restart R / RStudio (i.e. complete shutdown and restart)
diff --git a/vignette_snippets.md b/vignette_snippets.md
@@ -0,0 +1,13 @@
+# Vignette title
+
+```
+---
+title: "a good title"
+author: "Robert M Flight"
+date: "`r Sys.time()`"
+commit: "`r substr(git2r::branch_target(git2r::head(git2r::repository())), 1, 8)`"
+output: 
+  pdf_document: 
+    toc: yes
+---
+```
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -17,8 +17,8 @@ Use `cmdscale` on the proximities to look at how the samples behave in `RF`.
 rf_model <- randomForest(x ...., proximity = TRUE)
 # generate MDS scaling of proximities
 rf_sep <- stats::cmdscale(1 - rf_model$proximity, k = 2, eig = TRUE) # two components, using eigenvalue based 
-# data.frames are nicer to work with
-rf_sep <- as.data.frame(rf_sep)
+# data.frames are nicer to work with, but just need the points from cmdscale
+rf_sep <- as.data.frame(rf_sep$points)
 names(rf_sep) <- c("dim1", "dim2")
 
 # add your class information so can see how classes behave relative to one another using coloring (or shape, etc)

diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -4,4 +4,25 @@
 
 ```r
 + theme(axis.text.x = element_text(angle = 90))
+```
+
+# Random Forest
+
+## Separability plot
+
+Use `cmdscale` on the proximities to look at how the samples behave in `RF`.
+
+```r
+# generate model
+rf_model <- randomForest(x ...., proximity = TRUE)
+# generate MDS scaling of proximities
+rf_sep <- stats::cmdscale(1 - rf_model$proximity, k = 2, eig = TRUE) # two components, using eigenvalue based 
+# data.frames are nicer to work with
+rf_sep <- as.data.frame(rf_sep)
+names(rf_sep) <- c("dim1", "dim2")
+
+# add your class information so can see how classes behave relative to one another using coloring (or shape, etc)
+rf_sep$class <- factor_of_classes
+
+ggplot(rf_sep, aes(x = dim1, y = dim2, color = class) + geom_point()
 ```
diff --git a/tips_and_tricks.md b/tips_and_tricks.md
@@ -1,5 +1,7 @@
 # ggplot2
 
+## Rotate axis tick labels 90 degrees
+
 ```r
 + theme(axis.text.x = element_text(angle = 90))
 ```
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		If you want to know how many lines of code are in