diffHeatmap-methods: diffHeatmap

In ericaenjoy3/RNA: RNA data analysis

Description

heatmap during or after differential analysis

Usage

diffHeatmap(tpm.value, col.idx, row.idx, pdffout, cutreek = NULL,
  cut.alg = NULL, rank.man = FALSE, log.it.already = FALSE,
  scale.it = TRUE, cluster_columns_par = TRUE, cluster_rows_par = TRUE,
  show_column_dend_par = TRUE, show_row_dend_par = FALSE, small = 0.05,
  ...)

## S4 method for signature 'matrix'
diffHeatmap(tpm.value, col.idx, row.idx, pdffout,
  cutreek = NULL, cut.alg = NULL, rank.man = FALSE,
  log.it.already = FALSE, scale.it = TRUE, cluster_columns_par = TRUE,
  cluster_rows_par = TRUE, show_column_dend_par = TRUE,
  show_row_dend_par = FALSE, small = 0.05, ...)

Arguments

tpm.value	A tpm matrix.
col.idx	Numeric or logical indices specifying columns to keep of the tpm matrix.
row.idx	Numeric or logical indices specifying rows to keep of the codetpm matrix.
pdffout	A character string specify pdf output file.
cutreek	A logical value indicating whether to perform clustering.
cut.alg	A string value of selecting the clustering algorithm "pam","hclust" or "emmix".
rank.man	A logical value indicating whether to perform manual ranking on the row.
log.it.already	A logical value indicating whether the tpm matrix is already log2 transformed.
scale.it	A logical value indicating whether to row standardize the tpm matrix.
cluster_columns_par	A logical value indicating whether to cluster the columns of the tpm matrix.
cluster_rows_par	A logical value indicating whether to cluster the rows of the tpm matrix.
show_column_dend_par	A logical value indicating whether to show the column dendrogram.
show_row_dend_par	A logical value indicating whether to show the row dendrogram.
small	A numeric value indicating the adjustment to the TPM values before log2 transformation.
...	Additional arguments to be passed to methods.

ericaenjoy3/RNA documentation built on May 28, 2019, 8:37 p.m.