Description Usage Arguments Value
View source: R/plotHeatmap_I.R
This function plots heat maps using given input matrix and group conditions
1 2 3 4 5 6 | plotHeatmap_I(condition = c("mutant", "wildtype"), geneES, group,
palette, legendName = "Gene expression", distance = "spearman",
method = "ward.D2", rowCluster = TRUE, colCluster = TRUE,
rowName = TRUE, colName = TRUE, title, s1 = 15, s2 = 4,
s3 = 11, s4 = 6, s5 = 12, s6 = 100, s7 = 2, s8 = 4, s9 = 2,
H = 11, W = 28, Date)
|
condition |
a character type vector of the grouping annotation indicated in the pData(geneES). |
geneES |
an ExpressionSet object containing the input matrix and annotation data(one column of SampleID and the other of Group) |
group |
a data frame with each column a different column annotation which needs to be added to the heatmap, rownames correspond to sample ID. |
palette |
a named list with color palettes for each annotation, each element in the list should be a named vector. |
legendName |
name of the legend, default is "Gene expression". |
distance |
a character type variable indicating the distance used for clustering. Default is "spearman". |
method |
a character type variable indicating the clustering method. Default is "ward.D2". |
rowCluster |
a logical variable indicating whether to cluster the rows. Default is TRUE. |
colCluster |
a logical variable indicating whether to cluster the columns. Default is TRUE. |
rowName |
a logical variable indicating whether to show the row names. Default is TRUE. |
colName |
a logical variable indicating whether to show the column names. Default is TRUE. |
title |
a character variable representing the title of the heatmap. |
s1 |
a numerical variable indicating the fontsize of legend title. Default is 15. |
s2 |
a numerical variable indicating the fontsize of row names. Default is 8. |
s3 |
a numerical variable indicating the fontsize of column names. Default is 12. |
s4 |
a numerical variable indicating the height and width of grid in defined unit of column legend. Default is 6. |
s5 |
a numerical variable indicating the width of the dendrogram for columns and rows. Default is 12. |
s6 |
a numerical variable indicating the width of space for rowname and colname annotations. Default is 100. |
s7 |
a numerical variable indicating the space between each top annotation. Default is 2. |
s8 |
a numerical variable indicating the height of each column annotation. Default is 4. |
s9 |
a numerical variable indicating the space between heatmap body and annotations. Default is 2. |
H |
a numerical variable indicating the height of saved figure. Default is 15. |
W |
a numerical variable indicating the width of save figure. Default is 15. |
Date |
a Date object obtained from Sys.Date |
a "HeatmapList" class object.
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