plotMDS: Plots MDS

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

Plots MDS

Description

Plots MDS

Usage

plotMDS(
  df = NULL,
  id = NULL,
  label_scheme_sub = NULL,
  choice = "cmdscale",
  dist_co = log2(1),
  adjEucDist = FALSE,
  method = "euclidean",
  p = 2,
  k = 3,
  dimension = 2,
  folds = 1,
  show_ids = FALSE,
  show_ellipses = FALSE,
  col_group = NULL,
  col_color = NULL,
  col_fill = NULL,
  col_shape = NULL,
  col_size = NULL,
  col_alpha = NULL,
  color_brewer = NULL,
  fill_brewer = NULL,
  size_manual = NULL,
  shape_manual = NULL,
  alpha_manual = NULL,
  scale_log2r = TRUE,
  complete_cases = FALSE,
  filepath = NULL,
  filename = NULL,
  center_features = TRUE,
  scale_features = TRUE,
  theme = NULL,
  anal_type = "MDS",
  ...
)

Arguments

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.
choice	Character string; the MDS method in c("cmdscale", "isoMDS"). The default is "cmdscale".
dist_co	Numeric; The cut-off in the absolute distance measured by d = abs(x_i - x_j). Data pairs, x_i and x_j, with corresponding d smaller than dist_co will be excluded from distance calculations by dist. The default is no distance cut-off at dist_co = log2(1).
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.
method	Character string; the distance measure in one of c("euclidean", "maximum", "manhattan", "canberra", "binary") for dist. The default method is "euclidean".
p	Numeric; The power of the Minkowski distance in dist. The default is 2.
k	Numeric; The desired dimension for the solution passed to cmdscale. The default is 3.
dimension	Numeric; The desired dimension for pairwise visualization. The default is 2.
folds	Not currently used. Integer; the degree of folding data into subsets. The default is one without data folding.
show_ids	Logical; if TRUE, shows the sample IDs in MDS/PCA plots. The default is TRUE.
show_ellipses	Logical; if TRUE, shows the ellipses by sample groups according to col_group. The default is FALSE.
col_group	Character string to a column key in expt_smry.xlsx. Samples corresponding to non-empty entries under col_group will be used for sample grouping in the indicated analysis. At the NULL default, the column key Group will be used. No data annotation by groups will be performed if the fields under the indicated group column is empty.
col_color	Character string to a column key in expt_smry.xlsx. Values under which will be used for the color aesthetics in plots. At the NULL default, the column key Color will be used. If NA, bypasses the aesthetics (a means to bypass the look-up of column Color and handle duplication in aesthetics).
col_fill	Character string to a column key in expt_smry.xlsx. Values under which will be used for the fill aesthetics in plots. At the NULL default, the column key Fill will be used. If NA, bypasses the aesthetics (a means to bypass the look-up of column Fill and handle duplication in aesthetics).
col_shape	Character string to a column key in expt_smry.xlsx. Values under which will be used for the shape aesthetics in plots. At the NULL default, the column key Shape will be used. If NA, bypasses the aesthetics (a means to bypass the look-up of column Shape and handle duplication in aesthetics).
col_size	Character string to a column key in expt_smry.xlsx. Values under which will be used for the size aesthetics in plots. At the NULL default, the column key Size will be used. If NA, bypasses the aesthetics (a means to bypass the look-up of column Size and handle duplication in aesthetics).
col_alpha	Character string to a column key in expt_smry.xlsx. Values under which will be used for the alpha (transparency) aesthetics in plots. At the NULL default, the column key Alpha will be used. If NA, bypasses the aesthetics (a means to bypass the look-up of column Alpha and handle duplication in aesthetics).
color_brewer	Character string to the name of a color brewer for use in ggplot2::scale_color_brewer, i.e., color_brewer = Set1. At the NULL default, the setting in ggplot2 will be used.
fill_brewer	Character string to the name of a color brewer for use in ggplot2::scale_fill_brewer, i.e., fill_brewer = Spectral. At the NULL default, the setting in ggplot2 will be used.
size_manual	Numeric vector to the scale of sizes for use in ggplot2::scale_size_manual, i.e., size_manual = c(8, 12). At the NULL default, the setting in ggplot2 will be used.
shape_manual	Numeric vector to the scale of shape IDs for use in ggplot2::scale_shape_manual, i.e., shape_manual = c(5, 15). At the NULL default, the setting in ggplot2 will be used.
alpha_manual	Numeric vector to the scale of transparency of objects for use in ggplot2::scale_alpha_manual , i.e., alpha_manual = c(.5, .9). At the NULL default, the setting in ggplot2 will be used.
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.
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.
center_features	Logical; if TRUE, adjusts log2FC to center zero by features (proteins or peptides). The default is TRUE. Note the difference to data alignment with method_align in standPrn or standPep where log2FC are aligned by observations (samples).
scale_features	Logical; if TRUE, adjusts log2FC to the same scale of variance by features (protein or peptide entries). The default is TRUE. Note the difference to data scaling with scale_log2r where log2FC are scaled by observations (samples).
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
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. Additional parameters for ggsave: width, the width of plot; height, the height of plot ...

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.