inst/extdata/examples/prnEucDist_.R

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

\donttest{
# ===================================
# Euclidean distance
# ===================================

## !!!require the brief working example in `?load_expts`

## global option
scale_log2r <- TRUE

pepEucDist(
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),
  width = 14,
  height = 12,
)

prnEucDist(
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),

  # arguments for `pheatmap`
  display_numbers = TRUE,
  number_color = "grey30",
  number_format = "%.1f",
  clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean",
  fontsize = 16,
  fontsize_row = 20,
  fontsize_col = 20,
  fontsize_number = 8,
  cluster_rows = TRUE,
  show_rownames = TRUE,
  show_colnames = TRUE,
  border_color = "grey60",
  cellwidth = 24,
  cellheight = 24,
  
  filter_prots_by = exprs(prot_n_pep >= 5),
  filename = "filter.png",
)

## additional row filtration by pVals (proteins, impute_na = FALSE)
# if not yet, run prerequisitive significance tests at `impute_na = FALSE`
pepSig(
  impute_na = FALSE, 
  W2_bat = ~ Term["(W2.BI.TMT2-W2.BI.TMT1)", 
                  "(W2.JHU.TMT2-W2.JHU.TMT1)", 
                  "(W2.PNNL.TMT2-W2.PNNL.TMT1)"],
  W2_loc = ~ Term_2["W2.BI-W2.JHU", 
                    "W2.BI-W2.PNNL", 
                    "W2.JHU-W2.PNNL"],
  W16_vs_W2 = ~ Term_3["W16-W2"], 
)

prnSig(impute_na = FALSE)

# (`W16_vs_W2.pVal (W16-W2)` now a column key)
prnEucDist(
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),
  width = 14,
  height = 12,
  filter_by = exprs(`W16_vs_W2.pVal (W16-W2)` <= 1e-6), 
  filename = pvalcutoff.png, 
)

# analogous peptides
pepEucDist(
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),
  width = 14,
  height = 12,
  filter_by = exprs(`W16_vs_W2.pVal (W16-W2)` <= 1e-6), 
  filename = pvalcutoff.png, 
)

## additional row filtration by pVals (proteins, impute_na = TRUE)
# if not yet, run prerequisitive NA imputation
pepImp(m = 2, maxit = 2)
prnImp(m = 5, maxit = 5)

# if not yet, run prerequisitive significance tests at `impute_na = TRUE`
pepSig(
  impute_na = TRUE, 
  W2_bat = ~ Term["(W2.BI.TMT2-W2.BI.TMT1)", 
                  "(W2.JHU.TMT2-W2.JHU.TMT1)", 
                  "(W2.PNNL.TMT2-W2.PNNL.TMT1)"],
  W2_loc = ~ Term_2["W2.BI-W2.JHU", 
                    "W2.BI-W2.PNNL", 
                    "W2.JHU-W2.PNNL"],
  W16_vs_W2 = ~ Term_3["W16-W2"], 
)

prnSig(impute_na = TRUE)

prnEucDist(
  impute_na = TRUE,
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),
  width = 14,
  height = 12,
  filter_by = exprs(`W16_vs_W2.pVal (W16-W2)` <= 1e-6), 
  filename = filpvals_impna.png, 
)

# analogous peptides
pepEucDist(
  impute_na = TRUE,
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),
  width = 14,
  height = 12,
  filter_by = exprs(`W16_vs_W2.pVal (W16-W2)` <= 1e-6), 
  filename = filpvals_impna.png, 
)

## custom color
pepEucDist(
  impute_na = TRUE,
  annot_cols = c("Group", "Color", "Alpha", "Shape"),
  annot_colnames = c("Group", "Lab", "Batch", "WHIM"),
  width = 14,
  height = 12,
  filter_by = exprs(`W16_vs_W2.pVal (W16-W2)` <= 1e-6), 
  color = colorRampPalette(c("blue", "white", "red"))(500),
  filename = my_palette.png, 
)

## Not run: 
prnEucDist(
  col_color = "column_key_not_existed",
  col_shape = "another_missing_column_key",
  annot_cols = c("bad_column_key", "yet_another_bad_column_key")
)
## End(Not run)
}