comparison mqppep_anova_script.Rmd @ 4:0ab632432798 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1

3:6f51e262d84d

  # what should be the primary criterion to eliminate excessive heatmap rows
  intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
  # should correlation among substrates be used (rather than covariance)
  correlateSubstrates:  TRUE
  # only show covariance among variables having variance > 1
  filterCovVarGT1:      TRUE
  # maximum number of residues to display for ppeps in rownames or columnames
  ppepTruncN:           10
  # maximum number of characters of subgenes to display in rownames or columnames
  subgeneTruncN:        10
  # maximum number of characters for paste(subgene, ppep) for enrichment plots

  # look-up tables for kinase descriptions
  kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
  kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
  # should debugging trace messages be printed?
  showEnrichedSubstrates: FALSE
  # should debugging nb/nbe messages be printed?
  printNBMsgs:          FALSE
  #printNBMsgs:          TRUE
  # should row-scaling be applied to heatmaps: "none" or "row"
  defaultHeatMapRowScaling: !r c("none", "row")[1]
  # how missing values be displayed on heat maps: "NA" or " "
  heatMapNAcellNote:    !r c(" ", "NA")[1]
  # how missing values be displayed on heat maps: "NA" or " "

  # should debugging trace messages be printed?
  printTraceMsgs:       FALSE
  # when debugging files are needed, set debugFileBasePath to the path
  #   to the directory where they should be written
  debugFileBasePath:    !r if (TRUE) NULL else "test-data"
---

```{r setup, include = FALSE, results = 'asis'}

# simple debug messaging

             WHERE gene IN (SELECT kinase FROM enriched_kinases)
           ),
           p_value_data
         WHERE ppep = phosphopeptide
         GROUP BY kinase, ppep
         ORDER BY kinase, ppep, p_value_data.quality DESC
      "),
      justification = "l l l l l l l",
      centered = TRUE,
      caption = "labeled substrates of enriched kinases",
      anchor = c(const_table_anchor_p, const_table_anchor_t),

4:0ab632432798

  # what should be the primary criterion to eliminate excessive heatmap rows
  intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
  # should correlation among substrates be used (rather than covariance)
  correlateSubstrates:  TRUE
  # only show covariance among variables having variance > 1
  filterCovVarGT1:      FALSE
  # maximum number of residues to display for ppeps in rownames or columnames
  ppepTruncN:           10
  # maximum number of characters of subgenes to display in rownames or columnames
  subgeneTruncN:        10
  # maximum number of characters for paste(subgene, ppep) for enrichment plots

  # look-up tables for kinase descriptions
  kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
  kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
  # should debugging trace messages be printed?
  showEnrichedSubstrates: FALSE
  # should row-scaling be applied to heatmaps: "none" or "row"
  defaultHeatMapRowScaling: !r c("none", "row")[1]
  # how missing values be displayed on heat maps: "NA" or " "
  heatMapNAcellNote:    !r c(" ", "NA")[1]
  # how missing values be displayed on heat maps: "NA" or " "

  # should debugging trace messages be printed?
  printTraceMsgs:       FALSE
  # when debugging files are needed, set debugFileBasePath to the path
  #   to the directory where they should be written
  debugFileBasePath:    !r if (TRUE) NULL else "test-data"
  # should debugging nb/nbe messages be printed?
  printNBMsgs:          FALSE
  #printNBMsgs:          TRUE
---

```{r setup, include = FALSE, results = 'asis'}

# simple debug messaging

             WHERE gene IN (SELECT kinase FROM enriched_kinases)
           ),
           p_value_data
         WHERE ppep = phosphopeptide
         GROUP BY kinase, ppep
         ORDER BY kinase, p_value_data.quality DESC
      "),
      justification = "l l l l l l l",
      centered = TRUE,
      caption = "labeled substrates of enriched kinases",
      anchor = c(const_table_anchor_p, const_table_anchor_t),