add analysis workflow integration

[lthealy]

added arg10 (sampInfo.csv) to align calls, also added analytic call to both singularity and docker formats.

This version expects you to be using sbu_bmi/til_align branch align2analyze commit c2a94ef03b6f0ba5226edfd2bcf46af9062b758a

[kaczmarj]

thanks. i'll test this.

[kaczmarj]

i'm getting an error when using the sample.csv at https://github.com/SBU-BMI/til_align/blob/align2analyze/example/sampInfo.csv

[1] "TIL Algorithm (Threshold): Frontiers InceptionV4: 0.1"
[1] "=========== Params after R parsing, if any misalignment please check your flags ==========="
$algorithm
[1] "inceptionv4"

$tilDir
[1] "/data/results-tils"

$tilThresh
[1] 0.1

$cancDir
[1] "/data/results-tumor"

$cancThresh
[1] 0.5

$sampFile
[1] ""

$outputFile
[1] "output.csv"

$outputDir
[1] "/data/results-tilalign/"

$writePNG
[1] TRUE

$sampInfo
[1] "/data/sample_info.csv"

[1] "Sample 1: 1.74747474747475"
[1] "Sample 2: 1.75"
[1] "Sample 3: 1.75"
[1] "Sample 4: 1.75"
null device 
          1 
Error in is.data.frame(y) : object 'slideID' not found
Calls: <Anonymous> ... auto_copy -> same_src -> same_src.data.frame -> is.data.frame
Execution halted

[lthealy]

oh yea thats just a mistype of the join function at the end of commandLineAlign.R. fixed with align2analyze commit 0f945369a7660da39d63f4e90eeec67c5371341d

[kaczmarj]

i get this error when running the survival analysis r script. no output is written. i'm using the example sample info csv at https://github.com/SBU-BMI/til_align/blob/align2analyze/example/sampInfo.csv

$csvPath
[1] "/data/outputs/output.csv"

$survTime
[1] "survivalA"

$survCensor
[1] "censorA.0yes.1no"

$outputFormat
[1] "pdf_document"

processing file: Descriptive_Statistics.rmd
  |...                                                                   |   5%
   inline R code fragments

  |......                                                                |   9%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |..........                                                            |  14%
  ordinary text without R code

  |.............                                                         |  18%
label: load (with options) 
List of 1
 $ include: logi FALSE

  |................                                                      |  23%
  ordinary text without R code

  |...................                                                   |  27%
label: unnamed-chunk-1 (with options) 
List of 1
 $ fig.height: num 4

  |......................                                                |  32%
   inline R code fragments

  |.........................                                             |  36%
label: unnamed-chunk-2
Quitting from lines 67-83 (Descriptive_Statistics.rmd) 
Error in chisq.test(chi) : at least one entry of 'x' must be positive
Calls: <Anonymous> ... eval_with_user_handlers -> eval -> eval -> chisq.test
In addition: Warning messages:
1: Removed 4 rows containing non-finite values (stat_bin). 
2: In chisq.test(chi) : Chi-squared approximation may be incorrect
3: In chisq.test(chi) : Chi-squared approximation may be incorrect

[lthealy]

yea we should probably require a minimum strata size or else it skips the stat tests and just makes the figures. I'll make the changes and a specific issue

[kaczmarj]

replaced by #7