% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/plot_heatmap_features_by_clusters.R

\name{plot_heatmap_features_by_clusters}

\alias{plot_heatmap_features_by_clusters}

\title{Plot an heatmap of feature values in cell clusters}

\usage{

plot_heatmap_features_by_clusters(

scMuffinList = NULL,

feature_source = NULL,

partition_id = NULL,

significance_matrix = NULL,

sig_threshold = 0.05,

file = NULL,

width = 180,

height = 180,

units = "mm",

res = 300,

scale = FALSE,

pal = NULL,

na_col = "black",

X_abs_max = NULL,

...

)

}

\arguments{

\item{scMuffinList}{scMuffinList object}

\item{feature_source}{It can be a "mean", "gss" or a numeric matrix (clusters-by-features). If "mean", the data.frame with average feature values among clusters will be used (default); if "gene_set_scoring", the average gene set values among clusters will be used.}

\item{partition_id}{identifier of the partition to be considered}

\item{significance_matrix}{optional significance matrix (clusters-by-features) of the same size of the data specified by means of feature_source}

\item{sig_threshold}{significance threshold}

\item{file}{File name to save the figure as png file}

\item{width}{image width}

\item{height}{image height}

\item{units}{image units}

\item{res}{image resolution}

\item{scale}{whether to scale the features}

\item{pal}{color palette. Default to rev(pals::brewer.rdylbu(10)) (negative values) or pals::brewer.ylorrd(5)) (positive values)}

\item{na_col}{color for NA values}

\item{X_abs_max}{maximum absolute value permitted, useful to avoid the effect of outliers over colors}

\item{...}{further arguments to ComplexHeatmap::Heatmap}

}

\description{

Plot an heatmap of feature values in cell clusters

}