Description Usage Arguments Details Author(s) Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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,
...)
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data |
Data, file name or numeric dataframe/matrix to plot a heatmap.
For example " |
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 |
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 |
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_col |
Matrix or file with annotations of columns,
for example " |
annot_row_color |
Matrix or file with colors for annotation
in row, for example " |
annot_col_color |
Matrix or file with colors for annotation in column,
for example " |
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. |
Multiple types of file(.txt, .csv, .xls, .xlsx or tab limited file) or a matrix/dataframe is accepted as input.
Vaishali Tumulu and Sivasish Sindiri
Maintainer: Sivasish Sindiri <sentisci@gmail.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | # 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)
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