df |
The name of a primary data file. By default, it will be determined
automatically after matching the types of data and analysis with an
id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A
primary file contains normalized peptide or protein data and is among
c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt",
"Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses
require the fields of significance p-values, the df will be one of
c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt",
"protein_impNA_pVal.txt").
|
id |
Character string; one of pep_seq, pep_seq_mod,
prot_acc and gene.
|
label_scheme_sub |
A data frame. Subset entries from label_scheme
for selected samples.
|
adjEucDist |
Logical; if TRUE, adjusts the inter-plex Euclidean
distance by 1/sqrt(2) at method = "euclidean". The option
adjEucDist = TRUE may be suitable when reference samples from
each TMT plex undergo approximately the same sample handling process as the
samples of interest. For instance, reference samples were split at
the levels of protein lysates. Typically, adjEucDist = FALSE if
reference samples were split near the end of a sample handling
process, for instance, at the stages immediately before or after TMT
labeling. Also see online
README, section MDS for a brief
reasoning.
|
scale_log2r |
Logical; if TRUE, adjusts log2FC to the same scale
of standard deviation across all samples. The default is TRUE. At
scale_log2r = NA, the raw log2FC without normalization will
be used.
|
complete_cases |
Logical; if TRUE, only cases that are complete with no
missing values will be used. The default is FALSE.
|
annot_cols |
A character vector of column keys in expt_smry.xlsx.
The values under the selected keys will be used to color-code sample IDs on
the top of the indicated plot. The default is NULL without column
annotation.
|
annot_colnames |
A character vector of replacement name(s) to
annot_cols. The default is NULL without name replacement.
|
filepath |
A file path to output results. By default, it will be
determined automatically by the name of the calling function and the value
of id in the call.
|
filename |
A representative file name to outputs. By default, the
name(s) will be determined automatically. For text files, a typical file
extension is .txt. For image files, they are typically saved via
ggsave or pheatmap where the
image type will be determined by the extension of the file name.
|
anal_type |
Character string; the type of analysis that are preset for
method dispatch in function factories. The value will be determined
automatically. Exemplary values include anal_type = c("PCA",
"Corrplot", "EucDist", "GSPA", "Heatmap", "Histogram", "MDS", "Model",
"NMF", "Purge", "Trend", "LDA", ...).
|
... |
filter_: Variable argument statements for the row filtration
against data in a primary file linked to df. See also
normPSM for the format of filter_ statements.
arrange_: Variable argument statements for the row ordering against
data in a primary file linked to df. See also prnHM for
the format of arrange_ statements.
Additional parameters for
plotting:
width, the width of plot
height, the height
of plot
Additional arguments for pheatmap:
cluster_rows, clustering_method, clustering_distance_rows...
Notes about pheatmap:
annotation_col disabled; instead use keys indicated in annot_cols
annotation_row disabled; instead use keys indicated in annot_rows
|
