fheatmap (version 1.0.1)

Fanstatic Heatmap: R Function to Draw Heatmaps with Colored Dendogram

Description

R function to plot high quality, elegant heatmap using 'ggplot2' graphics . Some of the important features of this package are, coloring of row/column side tree with respect to the number of user defined cuts in the cluster, add annotations to both columns and rows, option to input annotation palette for tree and column annotations and multiple parameters to modify aesthetics (style, color, font) of texts in the plot.

Usage

fheatmap(data, header = T, scale = F, title = NA, title_fontsize = 6, title_color
= "black", title_font_style = "", title_fontface = "plain", rowname = T, breaks
= NULL, mat_color = NULL, cell_border = T, cell_border_col = "slategrey", 
cluster_rows = F, cluster_cols = T, cut_rowtree = 0, cut_coltree = 0, 
display_tree_col = T, display_tree_row = F, cluster_distance_rows = "euclidean",
cluster_distance_cols = "euclidean", clustering_method = "ward.D", 
annotation_palette = NULL, npalette_col = 5, annotation_row = NULL, annotation_col
= NULL, annot_row_color = NULL, annot_col_color = NULL, display_colnames = T, 
display_rownames = T, fontsize = 4, row_fontsize = fontsize, col_fontsize =
fontsize,names_font_style = "", names_fontface = "plain", names_color = "black",
legend_fontsize = fontsize, legend_font_style = "", legend_fontface = "plain", 
legend_color = "black", mat_legend_size = fontsize, display_number = F, seed = 13,
...)

Arguments

data

Data, file name or numeric dataframe/matrix to plot a heatmap. For example "fheatmap_data".

header

Logical, determining if the data file contains the names of the variables as its first line. (Default: TRUE)

scale

To standardize the given dataframe/matrix. (Default: FALSE)

title

Title of the heatmap. (Default: NA)

title_fontsize

Fontsize of the title. (Default: 6)

title_color

Color of the title. (Default: black)

title_font_style

Fontstyle of the title.

title_fontface

Fontface of the title. (Default: plain)

rowname

Logical determining if the file contains row names as its first column. (Default: TRUE)

breaks

A sequence of numbers that covers the range of values in matrix and is one element longer than mat_color vector. It is useful to assign different colors to different set of values.If value is NULL then the breaks are calculated automatically.

mat_color

Vector of colors used in heatmap. If value is NULL colors are calculated automatically.(Default: "green", "yellow","red")

cell_border

Logical determining if to draw border for each cells. not. (Default: FALSE)

cell_border_col

String color of the border .(Default: Grey)

cluster_rows

Logical determining if clustering in rows to be done or not. (Default: FALSE)

cluster_cols

Logical determining if clustering in columns to be done or not. (Default: TRUE)

cut_rowtree

Numeric value(N) to color N clusters in row dendogram. (Default: 0)

cut_coltree

Numeric value(N) to color N clusters in column dendogram. (Default: 0)

display_tree_col

Logical determining if column dendogram to be shown. (Default: TRUE)

display_tree_row

Logical determining if row dendogram to be shown. (Default: FALSE)

cluster_distance_rows

Distance measure used in clustering rows. Possible values are "correlation" for Pearson correlation and all the distances supported by dist, such as "euclidean", etc. (Default: "Euclidean")

cluster_distance_cols

Distance measure used in clustering columns. Possible values are same, as for clustering_distance_rows. (Default: "Euclidean")

clustering_method

Clustering method used. For Clustering methods refer the same values as mentioned in hclust. (Default: "ward.D")

annotation_palette

RColorBrewer palette for colors of row & column annotations.(Default: NULL) Distinct color is selected for each feature in anotation. Use "seed" parameter to fix random selection of colors. Either annotation_palette or aannotation color file can be given . (Default: NULL)

npalette_col

Numeric(N) If "annotation_palette" given ,then N distinct colors are selected from annotation_palette.Minimum 3, maximum depending on palette. (Default: 5)

annotation_row

Matrix or file with annotations of rows, for example "annotation_row" .Each column defines the features for a specific row. The rows in the data and columns in the annotation are matched using corresponding row and column names. Note that color schemes takes into account if variable is continuous or discrete. If NULL then annotation for row is not drawn.(Default: NULL)

annotation_col

Matrix or file with annotations of columns, for example "annotation_col" . Each row defines the features for a specific column. The columns in the data and rows in the annotation are matched using corresponding row and column names. Note that color schemes takes into account if variable is continuous or discrete. If NULL then annotation for columns is not drawn.(Default: NULL)

annot_row_color

Matrix or file with colors for annotation in row, for example "annotation_row_color" . If a file is given then row names and column names of annotation in row should be given in the first row & column respectively. If NULL then default colors are printed. (Default: NULL)

annot_col_color

Matrix or file with colors for annotation in column, for example "annotation_col_color". If a file is given then row names and column names of annotation in column should be given in the first row & column respectively. If NULL then default colors are printed. (Default: NULL)

display_colnames

Logical determining if column names to be shown or not. (Default: TRUE)

display_rownames

Logical determining if row names to be shown or not. (Default: TRUE)

fontsize

Base fontsize for the heatmap. (Default: 4)

row_fontsize

Fontsize for row names . (Default: fontsize)

col_fontsize

Fontsize for column names . (Default: fontsize)

names_font_style

Fontstyle for row names and column names .

names_fontface

Fontface for row names and column names . (Default: "plain", "bold", "italic", "bold-italic")

names_color

Color for row names and column names .

legend_fontsize

Fontsize for legend annotation. (Default: fontsize)

legend_font_style

Fontstyle for legend annotations.

legend_fontface

Fontface for legend annotations.

legend_color

Color for legend annotations.

mat_legend_size

Fontsize for matrix legend. (Default: fontsize)

display_number

Logical determining if the numeric values are printed into the cells.

seed

Numeric(N) If "annotation_palette" given ,then random number N to fix random selection of colors from the given palette.

...

It is used to match unspecified formal arguments of a function.

Details

Multiple types of file(.txt, .csv, .xls, .xlsx or tab limited file) or a matrix/dataframe is accepted as input.

Examples

 # Draw heatmaps
 fheatmap(fheatmap_data, title="Example Heatmap", title_fontsize=15, 
          title_color="coral4",title_fontface="italic")
 fheatmap(fheatmap_data, display_number = TRUE)
 
 # Add custom matrix color
 library(gplots)
 breaks <- seq(min(fheatmap_data),max(fheatmap_data), by=0.05)
 matrix_color_vector <- colorpanel(n=length(breaks)-1,low="green",mid="black",
                                    high="red")
 fheatmap(fheatmap_data, mat_color=matrix_color_vector,cluster_rows=TRUE)
 
 #Font style 
 fheatmap(fheatmap_data,names_fontface="italic",names_color="brown",fontsize=6)
 
 #Draw Dendograms
 fheatmap(fheatmap_data, cluster_rows=TRUE, cut_rowtree=2, cut_coltree=2, 
          display_tree_row=TRUE)
 
 # Generate annotations
 fheatmap(fheatmap_data, annotation_row=annotation_row,
          annotation_col=annotation_col)
 fheatmap(fheatmap_data, annotation_row=annotation_row, 
          annotation_col=annotation_col, 
          annot_row_color=annotation_row_color, 
          annot_col_color=annotation_col_color)
 fheatmap(fheatmap_data, annotation_row=annotation_row, 
          annotation_col=annotation_col,annotation_palette = "Dark2",
          npalette_col=5, seed=3)
 fheatmap(fheatmap_data, annotation_row=annotation_row,
          annotation_col=annotation_col,legend_fontsize=5,
          legend_fontface="bold", legend_color="red")
          
 #Complete heatmap
 fheatmap(fheatmap_data, cluster_rows=TRUE,display_tree_row=TRUE,
          title="Fantastic Heatmap",title_fontsize=15, 
          title_color="darkslateblue",title_fontface="italic",
          annotation_row=annotation_row,  annotation_col=annotation_col,
          annot_col_color=annotation_col_color,
          annot_row_color=annotation_row_color,names_font_style="mono",
          names_fontface="italic",names_color="coral4",fontsize=5,
          legend_fontsize=5,legend_fontface="italic",
          legend_color="coral4",cut_rowtree=2,cut_coltree=2,
          mat_legend_size=5)