plot_hm: A Function That Plots Heatmaps of Differentialy Expressed...

In fchuffar/epimedtools: Useful Tools Allowing Multi-Omics Analysis

A Function That Plots Heatmaps of Differentialy Expressed Genes Accros Conditions

Description

This function plots heatmaps of differentialy expressed genes across conditions.

Usage

plot_hm(exp_grp_key, case_fctr, anova_mw_res, study, ctrl_fctr, main,
  mw_pval = "mw_pval_adj", gene_pf_colname = "gene_name", key,
  PLOT_GS = FALSE, fc_thres = c(-1.5, -1.2, 1.2, 1.5),
  PLOT_PVAL = TRUE)

Arguments

exp_grp_key	the column name of the exprimental grouping to considere
case_fctr	The label of the group that we considere as differentialy expressed
anova_mw_res	A dataframe with ANOVA and Mann-Whitney results
study	An Reference classes object that contains data and metadata
ctrl_fctr	The label of the group that we considere as the reference
main	A character string to explicit the title of the plot
mw_pval	the the suffix the column name corresponding to the Mann-Whitney p-value used to
gene_pf_colname	A character string specifying the name of the platform column to use for the gene name
key	A character string that will suffix the column names of the resulting data frame
PLOT_GS	A boolean set to TRUE if genes names to be ploted
fc_thres	A vector of integer coprresponding to the foldchange thresholds
PLOT_PVAL	A boolean set to TRUE if ANOVA and Mann-Whitney need to be ploted

Value

probes used to plot the heatmap

fchuffar/epimedtools documentation built on Feb. 3, 2024, 2:21 a.m.