createSettingsJSON: createSettingsJSON

In decusInLabore/biologicSeqTools2: Seq Analysis Helper Functions

createSettingsJSON

Description

Method description

Usage

createSettingsJSON(
  obj = "object",
  df.data = "database.table",
  publicDataset = FALSE,
  defaultXcolName = NULL,
  defaultYcolName = NULL,
  timepointName = NULL,
  sample.order = "names(database.table)[grep('norm_counts', names(databse.table))]",
  heatmapSampleOrder = "lg2_avg vec",
  sample.names = "",
  count.sample.colors = "rainbow(length(sample.order))",
  ptm.colum = "display_ptm",
  count.table.headline = "PTM ratio H/L counts for all samples",
  count.table.sidelabel = "Counts",
  venn.slider.selector.strings = "c(\"contrast_x_logFC\", \"constrast_x_padj\")",
  plot.selection.strings =
    "c(\n    \"_logFC\",\n    \"_PCA_\",\n    \"_lg10p\"\n)",
  webSiteDir =
    "/camp/stp/babs/working/boeings/Stefan/protocol_files/github/biologic/src/experiments",
  upper_heatmap_limit = 3,
  lower_heatmap_limit = -3,
  heamap.headline.text = "heamap.headline.text",
  project_id = "project_id",
  primDataTable = "p123_rna_seq_table",
  pcaDbTable = NULL,
  pointer = "Gene Symbol:",
  samplesToExcludeFromTSdisplay = NULL
)

Arguments

samplesToExcludeFromTSdisplay

Sample names, as presented in dfDesign$sample.id, that are to be excluded from the timeseries display.

decusInLabore/biologicSeqTools2 documentation built on Nov. 21, 2024, 9:04 p.m.