BoutrosLab.plotting.general

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examples

Running examples in ‘BoutrosLab.plotting.general-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create.multipanelplot
> ### Title: Joins plots together
> ### Aliases: create.multipanelplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> set.seed(12345);
> # begin by creating the individual plots which will be combined into a multiplot
> dist <- data.frame(
+     a = rnorm(100, 1), 
+     b = rnorm(100, 3), 
+     c = rnorm(100, 5)
+     );
> 
> simple.data <- data.frame(
+     x = c(dist$a, dist$b, dist$c),
+     y = rep(LETTERS[1:3], each = 100)
+     );
> fill.squares <- matrix(c(1, 0, 0, 0, 1, 0, 0, 0, 1), ncol = 3, byrow = TRUE);
> rownames(fill.squares) <- c("Drug I only", "Drug II only" , "Drugs I & II");
> colnames(fill.squares) <- levels(factor(simple.data$y));
> 
> # Create plot # 1
> simple.boxplot <- create.boxplot(
+     formula = x ~ y,
+     data = simple.data,
+     xaxis.lab = c('','',''),
+     main.x = 0.57,
+     ylab.label = 'Sugar Level',
+     xlab.label = '',
+     col = 'lightgrey',
+     xaxis.tck = c(0,0),
+     yaxis.tck = c(1,0),
+     yaxis.lab = seq(-1,8,2) ,
+     yat = seq(-1,8,2),
+     left.padding = 0,
+     right.padding = 0,
+     lwd = 2
+     );
> 
> # Create plot # 2
> simple.heatmap <- create.heatmap(
+     x = t(fill.squares),
+     clustering.method = 'none',
+     shrink = 0.8,
+     yaxis.lab = c(3,2,3),
+     yaxis.tck = 1,
+     xaxis.lab = c('A','B','C'),
+     ylab.label = 'Drug Regimen',
+     xlab.label = 'Patient Group',
+     colour.scheme = c("white", "grey20"),
+     fill.colour = "white",
+     print.colour.key = FALSE,
+     left.padding = 0,
+     xaxis.tck = c(1,0),
+     right.padding = 0,
+     xaxis.rot = 0
+     );
> 
> create.multipanelplot(
+     # filename = tempfile(pattern = 'Multipanelplot_Simple', fileext = '.tiff'),
+     plot.objects = list(simple.boxplot,simple.heatmap), 
+     y.spacing = 1,  
+     ylab.axis.padding = 2, 
+     main = 'Simple', 
+     top.padding = 2,
+     resolution = 200
+     );
Error in basename(x) : a character vector argument expected
Calls: create.multipanelplot ... file_ext -> ifelse -> grepl -> is.factor -> basename
Execution halted

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘PlottingGuide.Rnw’ using knitr_notangle
Warning in remind_sweave(if (in.file) input, sweave_lines) :
  It seems you are using the Sweave-specific syntax in line(s) 2303, 2363; you may need Sweave2knitr("PlottingGuide.Rnw") to convert it to knitr

Quitting from PlottingGuide.Rnw:2303-2353 [auto-axis-scaling]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `basename()`:
! a character vector argument expected
---
Backtrace:
    x
 1. \-global create.auto.axis.examples()
 2.   \-BoutrosLab.plotting.general::create.multipanelplot(...)
 3.     \-BoutrosLab.plotting.general:::get.legend.height(...)
 4.       \-tools::file_ext(filename)
 5.         +-base::ifelse(...)
 6.         +-base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
 7.         | \-base::is.factor(x)
 8.         \-base::basename(x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PlottingGuide.Rnw' failed with diagnostics:
a character vector argument expected
--- failed re-building ‘PlottingGuide.Rnw’

SUMMARY: processing the following file failed:
  ‘PlottingGuide.Rnw’

Error: Vignette re-building failed.
Execution halted

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