comparison mqppep_anova_script.Rmd @ 25:f9cd87ac8006 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca

24:8582a9797c18

  kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
  regexSampleNames:     "\\.\\d+[A-Z]$"
  regexSampleGrouping:  "\\d+"
  show_toc:             true
  firstDataColumn:      "^Intensity[^_]"
  imputationMethod:     !r c("group-median", "median", "mean", "random")[4]
  meanPercentile:       1
  sdPercentile:         1.0
  imputedDataFilename:  "test-data/limbo/imputedDataFilename.txt"
  imputedQNLTDataFile:  "test-data/limbo/imputedQNLTDataFile.txt"
  anovaKseaMetadata:    "test-data/limbo/anovaKseaMetadata.txt"

  alphaFile:            "test-data/alpha_levels.tabular"
  inputFile:            "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
  preprocDb:            "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
  kseaAppPrepDb:        !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]

  inputFile:            "test-data/density_failure.preproc_tab.tabular"
  kseaAppPrepDb:        !r c(":memory:", "mqppep.sqlite")[2]
  latex_document: default
-->

              hm_heading_function     = cat_hm_heading,
              hm_main_title           =
                "log(intensities), row-scaled, unimputed, unnormalized",
              suppress_row_dendrogram = FALSE
            )
      }
    }
  }
}
cat("\\leavevmode\n")
cat("The adjusted ANOVA \\textit{p}-value is shown in parentheses
  after the phosphopeptide sequence.\n\n")
```

```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}

if (count_of_treatment_levels > 1) {

      # - 3 : non-significant kinases
      which_kinases = which_kinases
    )
    if (!is.null(plotted_kinases)) {
      cat("\\begin{center}\n")
      cat("Color intensity reflects $z$-score magnitudes; hue reflects $z$-score sign.  Asterisks reflect significance.\n")
      cat("\\end{center}\n")
    }
  } # end for (i in ...
} # end if (length ...

25:f9cd87ac8006

  kseaAppPrepDb:        !r c(":memory:", "test-data/mqppep.sqlite")[2]
  regexSampleNames:     "\\.\\d+[A-Z]$"
  regexSampleGrouping:  "\\d+"
  show_toc:             true
  firstDataColumn:      "^Intensity[^_]"
  imputationMethod:     !r c("group-median", "median", "mean", "random")[1]
  meanPercentile:       1
  sdPercentile:         1.0
  imputedDataFilename:  "test-data/limbo/imputedDataFilename.txt"
  imputedQNLTDataFile:  "test-data/limbo/imputedQNLTDataFile.txt"
  anovaKseaMetadata:    "test-data/limbo/anovaKseaMetadata.txt"

  alphaFile:            "test-data/alpha_levels.tabular"
  inputFile:            "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
  preprocDb:            "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
  kseaAppPrepDb:        !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
  regexSampleNames:     "\\.\\d+[A-Z]$"
  regexSampleGrouping:  "\\d+"

  inputFile:            "test-data/density_failure.preproc_tab.tabular"
  kseaAppPrepDb:        !r c(":memory:", "mqppep.sqlite")[2]
  latex_document: default
-->

              hm_heading_function     = cat_hm_heading,
              hm_main_title           =
                "log(intensities), row-scaled, unimputed, unnormalized",
              suppress_row_dendrogram = FALSE
            )
          if (number_of_peptides_found > 1) {
            cat("\\leavevmode\n")
            cat("The adjusted ANOVA \\textit{p}-value is shown in parentheses
              after the phosphopeptide sequence.\n\n")
          }
      }
    }
  }
}
cat("\\leavevmode\n")
```

```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}

if (count_of_treatment_levels > 1) {

      # - 3 : non-significant kinases
      which_kinases = which_kinases
    )
    if (!is.null(plotted_kinases)) {
      cat("\\begin{center}\n")
      cat("Color intensity reflects $z$-score magnitudes; hue reflects $z$-score sign.\n")
      if (which_kinases != const_ksea_nonastrsk_kinases)
        cat("Asterisks reflect significance.\n")
      cat("\\end{center}\n")
    }
  } # end for (i in ...
} # end if (length ...