diffHeatmap-methods: diffHeatmap

Description Usage Arguments

Description

heatmap during or after differential analysis

Usage

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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.