The markdownreports from vertesy

NewReport() function

When you want a new report only, but everything the same. (currently you rerun the setup+... function)
(If you only want to change OutDir, simply set it)
Add an option to setup_MarkdownReports() when you don't want any report file (but set all other variables) sth like: setup_MarkdownReports(, title = NULL)

Create 2 versions of the library: simple and advanced

2 versions

simple (4 beginners, static)
advanced (4 me, actively developed)

incrBottMarginBy BUG - it keeps adding to the bottom margin, until you call dev.off()

create_set_OutDir should change directory to OutDir by default

, setwd = T

...

if (setwd) { setwd(OutDir) }

Add 45˚ Label to other functions as well

taken from wbarplot. Maybe in one common function?

Some warnings at installation - Probably caused by Roxygen: unknown macro '\item' ; unexpected section header; unexpected END_OF_INPUT '

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
* installing *source* package 'MarkdownReports' ...
** R
** preparing package for lazy loading
** help
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_DF_RowColNames.Rd:17: unknown macro '\item'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_DF_RowColNames.Rd:19: unexpected section header '\description'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_DF_RowColNames.Rd:22: unexpected section header '\examples'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_DF_RowColNames.Rd:26: unexpected END_OF_INPUT '
'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_NamedVector.Rd:17: unknown macro '\item'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_NamedVector.Rd:19: unexpected section header '\description'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_NamedVector.Rd:22: unexpected section header '\examples'
Warning: /Users/.../MarkdownReports/MarkdownReports/man/MarkDown_Table_writer_NamedVector.Rd:26: unexpected END_OF_INPUT '
'
*** installing help indices
** building package indices
** testing if installed package can be loaded
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
* DONE (MarkdownReports)
Reloading installed MarkdownReports

Attaching package: 'MarkdownReports'

Note the modification date of the files read in (especially for metadata).

Add it to the read.simple.* functions


read.simple.* (..., ReportFileModification = F, ...)

if(ReportFileModification) {
       llogit(paste0("*" , paste(fname, file.info("Your_file")$mtime, sep="\t"), "*") )
}

Where to report?

At the end, in one table?
When the file is read in? -> I go for this, easier implementation.

Github PNG link is not correct, or at least not clear how it should work.

It is designed for the wiki, but the script is not there - hence I had to put the link manually.

     <!--The link below is parsed manual. The github integration is designed for the wiki, while this site is not there!-->

Set pdf title to script name by setup_logging_markdown() ?

Write the generating scriptname in it!

SO. Report logbook journal

Roxy: package creation

Upgrade Wiki

Add install & usage site
Add Function Overview site

add autolegend functionality to wplot

Use defaults for

bty
labels
colors

position

               legend = F, legend_poz = "topleft", legend_col = NULL, bty ="n"     ) {

Add SUM column to MarkDown_Table_writer_NamedVector()

MarkDown_Table_writer_NamedVector()

  MarkDown_Table_writer_NamedVector( ..., AppendSUMcolumn =F)

SUM column

MarkDown_Table_writer_DF_RowColNames()

  MarkDown_Table_writer_DF_RowColNames ( ..., AppendSUMcolumn =F, AppendSUMrow =F)

SUM column
SUM row

Add "copy path to clipboard" to wplot funcitons

Call oo() function.

Default no

Better way to set OutDir

Would be to use the scriptname without the extension by default

kollapse(ProjectDir, "/", gsub(x = scriptname, pattern = ".r$", replacement = "", ignore.case = T))

But where should `ProjectDir` come from?

Maybe:

if (exists(ProjectDir)) {
  OutDir = kollapse(ProjectDir, "/", gsub(x = scriptname, pattern = ".r$", replacement = "", ignore.case = T)) 
  any_print("OutDir is defined inside the ProjectDir: ", OutDir)
} else {
  OutDir = kollapse(getwd(), "/", gsub(x = scriptname, pattern = ".r$", replacement = "", ignore.case = T)) 
  any_print("OutDir is defined in your current working dir: ", OutDir)
}

Add "WriteOutTsv" feature to MarkDown_Table_writer_DF_RowColNames()

after renaming the funciton to sth more usefule

Demonstrate each plotting function with an example showing all its capabilities .

Add my workflow site to wiki

What I do
Script header
Backup
Image conversion
Typical directory
Github

add abline() to wplot function

Save sessioninfo into an invisible file for full reproducibility

Add this to setup_MarkdownReports() or somewhere later, where everything is loaded?
Add it to docs

writeLines(capture.output(sessionInfo()), ".sessionInfo.txt")

More consise naming of functions and paramters

Functions

Consistent names for Internal Functions ww.functionname
Rename functions to md_ ...
- only possible in v.3 for compatibility reasons

Function Parameters

scriptname instead of fname
xlab, ylab, col should be the same
- only possible in v.3 for compatibility reasons

Background Variables

Consistent names for Background Variables: b.varname

Else

Explain in the wiki

wstripchart() and wstripchart_list() cannot display subtitles

rename functions to md_ ...

rename functions to md_ ...

md_table.. is shorter

explain in the wiki

!!! Will be incompatible with previous script versions !!!

iround() seems to make rounding errors?

subs = iround(t(scale(t(subs))))

/Users/abelvertesy/Google_Drive/Spermatogenesis_Data/sp1_analysis_new/DiffExp3/MedianExpr_DE_r.tsv

wplot: lcol argument does not work for error bars

StdErr =c( 0, 219, 118, 78.8, 46.7, 52.7, 58, 64.9, 79.7, 73.1, 64.9, 66.1, 72.2, 58.3, 60.2 )
wplot(Optimal_Cluster_Count,  type="b", errorbar = T, upper = StdErr, lcol = 2)

tilted_text in wstripchart is not working: empty space

zz = list (
a = rnorm(10),
aa = rnorm(10),
aqq = rnorm(10)
)
wstripchart(zz, tilted_text = T, incrBottMarginBy = 3)

Explain the GitHub workflow

link to a png file that needs to be uploaded to GitHub-wiki under Reports/Folder-of-the-report/

Once you are satisfied with the layout of your report:

Revise your report once more to check if its understandable for others, axes labels, legends are correct, etc...
Copy the .md and all .pdf files in the subfolder autogenerated with the time stamp trailing its name
Convert all pdf files into .png (GitHub cannot display .pdf at the moment)
Copy the folder to your GitHub-wiki folder under Reports/
Remove the timestamp from the foldername
Upload to / Sync your github.wiki-s own repository (it is separate from your code repo)

If Images are not displayed, probably the link to them is not correct.

Check the .md file if the links are correct. Should look similar to this

   ![](Reports/YOURANALYSIS/YOURPLOT.png)

Add tilted_text option to whist

Use the title field to annotate each pdf with Keywords / tags. Make a (setup)function that does that

Tables: writing markdown and writing a tsv, should have an option to do the other one at the same time

If you log the table

MarkDown_Table_writer_DF_RowColNames( table, ... , WriteOut = FALSE )

if (WriteOut) { write.simple.tsv(table) }

...and if you write out

write.simple.tsv (table, ..., AddToMarkdownReport = FALSE )

if (AddToMarkdownReport) { MarkDown_Table_writer_DF_RowColNames((table) }

MarkDown_Table_writer...() should print the table written ou by default

In both functions:

MarkDown_Table_writer...( ...., print = T)

if (print == T) {print( XXX )}

My name should be changed on Zenodo: no accents. Next release should have a better title / description

Relase title:

MarkdownReports: An R function library to create scientific figures and reports easily. Update 2.2.

Rename function as file to file or memory to file

wvenn() function

Seems that there is no ideal package


create_set_OutDir("/Users/abelvertesy/Downloads/VennDiagram")
setwd(OutDir)
getwd()

install.packages("VennDiagram")
require("VennDiagram")

aaa =  list(
    a = c(1:4),
    b = c(1:7),
    a = c(4:11)
)

venn.diagram(aaa, imagetype = "png", filename = kollapse(substitute(aaa), ".png"))

New function to return a Markdown table to the command line, instead of writing it anywhere

Parse and print sth like this:

	1	2	3	4	5	CV
Means	0.12	0.18	0.11	0.11	0.88	1.2
Geometric Means	0.088	0.098	0.072	0.088	0.33	0.81
Medians	0.11	0.12	0.095	0.1	0.19	0.31

Add some pictures to the website so ppl can see what is it about!

Figure out, how to put in dependencies

require(VennDiagram)
require(vioplot)

Merge create_set_OutDir() and setup_logging_markdown() functions

Pass on the full path to setup_logging_markdown(), with optional alternative OutDir

In general, any envir variables defined, should be reported to the screen!

vline in wbarplot is not working

x = abs(rnorm(15))
wbarplot(x, vline=5)

x = abs(rnorm(15))
wbarplot(x, vline=1:15)

Scatterplot with 2D error bars in wplot()

incorporate error bars in sister function of wplot. Maybe in wplot itself.

Rename the project (wiki, code, website)

MarkdownReport.R written out as MarkdownReporter

Add A4 as a possible default output size for plots

You should default it in setup_MarkdownReports() and use the here defined global variable in the other functions.

Use theses as a start:

pdfA4plot_on <- function (pname = date(), ..., w = 8.27, h = 11.69, rows = 4, cols = 3, title = paste0(basename(fname), " by ", scriptname)) { # Print (multiple) plots to an (A4) pdf.
  assign("mfrow_default", par("mfrow"), fname, envir = .GlobalEnv)
  fname = kollapse(OutDir,"/" , pname, ".pdf")
  pdf(fname,width=w, height=h, title = title)
  par(mfrow = c(rows, cols))
  any_print(" ----  Don't forget to call the pair of this function to finish the pdf: pdfA4plot_off ()")
}

pdfA4plot_off <- function () {
  if (exists("mfrow_default")) {
    x = mfrow_default
  } else { x =  c(1,1)}
  par(mfrow = x)
  try(dev.off()) # close pdf
  oo();
}

Put a symlink to the directory of the website, to have only one read me file

It might not work: maybe it will sync out back

subscript_in_plots() is not working inside wstripchart()

wstripchart(Myh3_Expression_log2_ls, col = colors_age, pchlwd = 2, jitter = .4, pch=18, ylab =subscript_in_plots(quantity = "RPKM+1"))

it does work in the others!

Function to store parameters in a list

Make a function p that stores parameters in a list param as well as assign it globally.

p(threshold = 50) 
param$threshold
> 50

... and then log_settings_MarkDown can be called empty

 log_settings_MarkDown()

The function should check if
- param exists
- the name in param exists.

Reorganize Rfunctions (outsorce funcitons of mdLogger)

Make sure that functions are present only once... Maybe still refer to them in .Rfun... file
Maybe even separate them by the function of the function

Edit the project's own website to redirect to vertesy/MarkdownReports

Do it at the very end, it will be overwritten every time you load Readme.md

change the following links

view on github
maintained by
edit the website?

edit:

   subl /Users/abelvertesy/markdownreports.github.io/index.html

wbarplot(): cannot define ylim

Error in barplot.default(variable, ..., names.arg = xlb, main = main,  : 
  formal argument "ylim" matched by multiple actual arguments
Called from: barplot.default(variable, ..., names.arg = xlb, main = main, 
    sub = subtitle, col = col, las = 2, cex.names = cexNsize, 
    ylim = ylim)

wbarplot() tilted labels are not below the axis

Title of tables fall apart if not a simple proper variable is passed on

MarkDown_Table_writer_DF_RowColNames(t(as.dataframe(...)))

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