plotTrend: Plots trends

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

Plots trends

Description

Plots trends

Usage

plotTrend(
  id,
  col_group,
  col_order,
  label_scheme_sub,
  n_clust,
  scale_log2r,
  complete_cases,
  impute_na,
  df2 = NULL,
  filepath,
  filename,
  theme,
  ...
)

Arguments

id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
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_order	Character string to a column key in expt_smry.xlsx. Numeric values under which will be used for the left-to-right arrangement of samples in graphic outputs or top-to-bottom arrangement in text outputs. At the NULL default, the column key Order will be used. If values under column Order are left blank, samples will be ordered by their names.
label_scheme_sub	A data frame. Subset entries from label_scheme for selected samples.
n_clust	Numeric vector; the cluster ID(s) corresponding to anal_prnTrend for visualization. At the NULL default, all available cluster IDs will be used.
scale_log2r	Logical; at the TRUE default, input files with _Z[...].txt in name will be used. Otherwise, files with _N[...].txt in name will be taken. An error will be thrown if no files are matched under given conditions.
complete_cases	Logical; if TRUE, only cases that are complete with no missing values will be used. The default is FALSE.
impute_na	Logical; at the TRUE default, input files with _impNA[...].txt in name will be loaded. Otherwise, files without _impNA in name will be taken. An error will be thrown if no files are matched under given conditions.
df2	Character vector or string; the name(s) of secondary data file(s). An informatic task, i.e. anal_prnTrend(...) against a primary df generates secondary files such as Protein_Trend_Z_nclust6.txt etc. See also prnHist for the description of a primary df; normPSM for the lists of df and df2.
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, it will be determined automatically by the name of the current call.
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
...	filter2_: Variable argument statements for the row filtration against data in secondary file(s) of [...]Protein_Trend_[...].txt. See also prnGSPAHM for the format of filter2_ statements. arrange2_: Variable argument statements for the row ordering against data in secondary file(s) of [...]Protein_Trend_[...].txt. See also prnGSPAHM for the format of arrange2_ statements. Additional parameters for use in plot_ functions: ymin, the minimum y at log2 scale; ymax, the maximum y at log2 scale; ybreaks, the breaks in y-axis at log2 scale; nrow, the number of rows; width, the width of plot; height, the height of plot; color, the color of lines; alpha, the transparency of lines.

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