pairheatmap: Heatmap Comparison
In pairheatmap: A tool for comparing heatmaps
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
The main function for comparing heatmaps
Usage
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pairheatmap (data1, data2,
scale="none", dendrogram="both",
matDist=0.5, matrixBorderCol = "grey",
colorStyle="s1",
rowGroup=rowGroup,
orderRowGroup=NULL,
rowGroupColor=FALSE,
rowGroupColor.choice,
groupBorder="line",
groupBorder.selectList=list(),
groupBorder.lwd=3,
groupBorder.col="green",
rowNameColor="blue",
colNameColor="blue",
rowNameFontSize=7,
colNameFontSize=7,
rowNameGroupColor=NULL,
clusterMethod="complete", clusterMembers=NULL,
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=FALSE,
legend.pos="middle", legend.percent=0.5, legend.fontsize=7
)
Arguments
data1
numeric matrix 1. It is considered as the standard matrix.
data2
numeric matrix 2. Its row order is same as that in data1. Its column order is either same as that in data1 or use separate cluster method.
scale
character. It takes four values: "row", "col", "rowsep", "none"(default value). It indicates whether or not the data matrix is scaled in row/column direction. When "rowsep" is selected, the two data matrices are scaled separately in row direction.
dendrogram
character. It takes three values: "row", "col", "both"(default value). It indicates whether or not to draw the row/col/both dendrogram.
matDist
the separate distance between two data matrices. Default value is 0.5. If its value is 1, the distance between two matrices is exactly one data column.
matrixBorderCol
the color of the matrix border. Default value is "grey".
colorStyle
the color style for the matrix cell. It takes four values: "s1"(default value), "s2", "s3", "s4". s1 ranges from blue to red; s2 ranges from green to red; s3 uses a default color style from R package, pheatmap; s4 ranges from white to black.
rowGroup
Row group variable.
orderRowGroup
variable. The default value is "NULL". It is the row levels that should be ordered.
rowGroupColor
logical value. It takes two values: "TRUE", "FALSE". It indicates whether or not to draw the row group bar.
rowGroupColor.choice
character. It works when rowGroupColor is set as TRUE. The character length must match the unique groups in the rowGroup. If it is not specified, the colorStyle is used as default value.
groupBorder
character. It takes two values: "line"(default value), "rect". It controls the shape of the group border.
groupBorder.selectList
a list. It controls which group to be selected, which
includes four components, "xgroup.start", "xgroup.end", "ygroup.start" and "ygroup.end".
The selected groups will utilize the same graphical parameters as groupBorder.
groupBorder.lwd
numeric. Default value is 3. It controls the line width of the groupBorder.
groupBorder.col
character. Default value is "green". It controls the line color of the groupBorder.
rowNameColor
character string. Default value is "blue". It controls the label color of the row name.
colNameColor
character string. Default value is "blue". It controls the label color of the column name.
rowNameFontSize
numeric scalar. Default value is 7. It controls the font size of the row name.
colNameFontSize
numeric scalar. Default value is 7. It controls the font size of the column name.
rowNameGroupColor
character variable. The character length must match the
unique groups in the rowGroup. It controls the color of different groups of row names.
clusterMethod
character. It takes the follow values: "ward", "single", "complete"(default value),
"average", "mcquitty", "median" or "centroid".
clusterMembers
NULL or a vector. See function: "hclust" of the package "stats" for details.
clusterRow
logical. It takes two values: "TRUE"(default value), "FALSE". It indicates whether or not
to cluster rows.
clusterCol
logical. It takes two values: "TRUE"(default value), "FALSE". It indicates whether or not
to cluster columns.
clusterColTogether
logical. It takes two values: "TRUE", "FALSE"(default value). It indicates whether
or not the columns of data matrix 2 follows the same clustering order of that in data matrix 1.
If the column number of data matrix 2 is different from that of data matrix 1, only the columns
matching those of data matrix 1 are reordered.
legend.pos
character. It takes three values: "top", "middle"(default value), "bottom".
It controls the position of the legend.
legend.percent
numeric. It takes value from 0 to 1. Default value is 0.5. If its value is 1,
the height of the legend will be equal to the height of the heatmap.
legend.fontsize
numeric. Default value is 7. It controls the font size of the legend labels.
Details
This function compares two heatmaps and discovers links and patterns within and across groups. In the context of biology, group can be defined based on gene ontology or selected gene lists.
Value
Invisibly return the row and column index for two matrices.
Author(s)
Xiaoyong Sun
Examples
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## simple demo
chvalue <- pairheatmap(mtcars, mtcars)
chvalue
pairheatmap(mtcars, mtcars, scale="row")
pairheatmap(mtcars, mtcars[,1:5], scale="row")
pairheatmap(mtcars, mtcars[,1:5], scale="rowsep")
pairheatmap(mtcars, mtcars[,1:5], scale="col")
## row group bar
pairheatmap(mtcars, mtcars,
rowGroup=mtcars$gear,
rowNameFontSize=6,
colNameFontSize=6,
rowNameGroupColor=rev(c("blue", "green", "orange")),
rowNameColor="blue",
)
## group options
pairheatmap(mtcars, mtcars,
rowGroup=mtcars$gear,
orderRowGroup=c(5, 4,3)
)
## legend
pairheatmap(mtcars, mtcars,
legend.pos="middle", legend.percent=0.6, legend.fontsize=7)
## cluster analysis
pairheatmap(mtcars, mtcars, clusterMethod="ward", clusterRow=FALSE)
pairheatmap(mtcars, cbind(mtcars, mtcars), clusterColTogether=TRUE)
## selected groups
pairheatmap(mtcars, cbind(mtcars, mtcars),
groupBorder.selectList=
list(xgroup.start=c(2,7), xgroup.end=c(4,9),
ygroup.start=c(3,30), ygroup.end=c(10,32)
))
## more demo
pairheatmap(mtcars, mtcars, legend.percent=1, legend.pos="middle",
groupBorder.selectList=list(xgroup.start=c(2,7), xgroup.end=c(4,9), ygroup.start=c(3,30),
ygroup.end=c(10,32)))
pairheatmap(mtcars, mtcars, scale="row", colorStyle="s3",
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11),
ygroup.start=c(11), ygroup.end=c(15)),
legend.pos="top")
pairheatmap(mtcars, mtcars,
colorStyle="s4", rowGroup=mtcars$gear,
rowGroupColor=TRUE,
rowGroupColor.choice = rev(c("blue", "orange", "green")),
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
legend.pos="top", legend.percent=0.6, legend.fontsize=5, orderRowGroup=c(5, 4,3),
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=TRUE
)
mtcars2 <- mtcars[, rev(1:ncol(mtcars))]
pairheatmap(mtcars, mtcars2,
colorStyle="s1", rowGroup=mtcars$gear,
rowGroupColor=TRUE,
rowGroupColor.choice = rev(c("blue", "orange", "green")),
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
legend.pos="top", legend.percent=0.6, legend.fontsize=5, orderRowGroup=c(5, 4,3),
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=FALSE
)
pairheatmap(mtcars, mtcars,
dendrogram="row", colorStyle="s1", rowGroup=mtcars$am,
rowGroupColor=TRUE,
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
legend.pos="top", legend.percent=0.6, legend.fontsize=5,
orderRowGroup=c(0,1),
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=FALSE
)
Example output
Loading required package: grid
$rowInd
[1] 31 17 15 16 29 7 24 5 25 4 6 14 12 13 22 23 19 20 18 26 30 28 9 32 3
[26] 21 27 8 1 2 10 11
$colInd1
[1] 1 7 2 8 9 5 10 6 11 3 4
$colInd2
[1] 1 7 2 8 9 5 10 6 11 3 4
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
pairheatmap documentation built on May 2, 2019, 6:42 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
The main function for comparing heatmaps
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | pairheatmap (data1, data2,
scale="none", dendrogram="both",
matDist=0.5, matrixBorderCol = "grey",
colorStyle="s1",
rowGroup=rowGroup,
orderRowGroup=NULL,
rowGroupColor=FALSE,
rowGroupColor.choice,
groupBorder="line",
groupBorder.selectList=list(),
groupBorder.lwd=3,
groupBorder.col="green",
rowNameColor="blue",
colNameColor="blue",
rowNameFontSize=7,
colNameFontSize=7,
rowNameGroupColor=NULL,
clusterMethod="complete", clusterMembers=NULL,
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=FALSE,
legend.pos="middle", legend.percent=0.5, legend.fontsize=7
)
|
Arguments
data1 |
numeric matrix 1. It is considered as the standard matrix. |
data2 |
numeric matrix 2. Its row order is same as that in data1. Its column order is either same as that in data1 or use separate cluster method. |
scale |
character. It takes four values: "row", "col", "rowsep", "none"(default value). It indicates whether or not the data matrix is scaled in row/column direction. When "rowsep" is selected, the two data matrices are scaled separately in row direction. |
dendrogram |
character. It takes three values: "row", "col", "both"(default value). It indicates whether or not to draw the row/col/both dendrogram. |
matDist |
the separate distance between two data matrices. Default value is 0.5. If its value is 1, the distance between two matrices is exactly one data column. |
matrixBorderCol |
the color of the matrix border. Default value is "grey". |
colorStyle |
the color style for the matrix cell. It takes four values: "s1"(default value), "s2", "s3", "s4". s1 ranges from blue to red; s2 ranges from green to red; s3 uses a default color style from R package, pheatmap; s4 ranges from white to black. |
rowGroup |
Row group variable. |
orderRowGroup |
variable. The default value is "NULL". It is the row levels that should be ordered. |
rowGroupColor |
logical value. It takes two values: "TRUE", "FALSE". It indicates whether or not to draw the row group bar. |
rowGroupColor.choice |
character. It works when rowGroupColor is set as TRUE. The character length must match the unique groups in the rowGroup. If it is not specified, the colorStyle is used as default value. |
groupBorder |
character. It takes two values: "line"(default value), "rect". It controls the shape of the group border. |
groupBorder.selectList |
a list. It controls which group to be selected, which includes four components, "xgroup.start", "xgroup.end", "ygroup.start" and "ygroup.end". The selected groups will utilize the same graphical parameters as groupBorder. |
groupBorder.lwd |
numeric. Default value is 3. It controls the line width of the groupBorder. |
groupBorder.col |
character. Default value is "green". It controls the line color of the groupBorder. |
rowNameColor |
character string. Default value is "blue". It controls the label color of the row name. |
colNameColor |
character string. Default value is "blue". It controls the label color of the column name. |
rowNameFontSize |
numeric scalar. Default value is 7. It controls the font size of the row name. |
colNameFontSize |
numeric scalar. Default value is 7. It controls the font size of the column name. |
rowNameGroupColor |
character variable. The character length must match the unique groups in the rowGroup. It controls the color of different groups of row names. |
clusterMethod |
character. It takes the follow values: "ward", "single", "complete"(default value), "average", "mcquitty", "median" or "centroid". |
clusterMembers |
NULL or a vector. See function: "hclust" of the package "stats" for details. |
clusterRow |
logical. It takes two values: "TRUE"(default value), "FALSE". It indicates whether or not to cluster rows. |
clusterCol |
logical. It takes two values: "TRUE"(default value), "FALSE". It indicates whether or not to cluster columns. |
clusterColTogether |
logical. It takes two values: "TRUE", "FALSE"(default value). It indicates whether or not the columns of data matrix 2 follows the same clustering order of that in data matrix 1. If the column number of data matrix 2 is different from that of data matrix 1, only the columns matching those of data matrix 1 are reordered. |
legend.pos |
character. It takes three values: "top", "middle"(default value), "bottom". It controls the position of the legend. |
legend.percent |
numeric. It takes value from 0 to 1. Default value is 0.5. If its value is 1, the height of the legend will be equal to the height of the heatmap. |
legend.fontsize |
numeric. Default value is 7. It controls the font size of the legend labels. |
Details
This function compares two heatmaps and discovers links and patterns within and across groups. In the context of biology, group can be defined based on gene ontology or selected gene lists.
Value
Invisibly return the row and column index for two matrices.
Author(s)
Xiaoyong Sun
Examples
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 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | ## simple demo
chvalue <- pairheatmap(mtcars, mtcars)
chvalue
pairheatmap(mtcars, mtcars, scale="row")
pairheatmap(mtcars, mtcars[,1:5], scale="row")
pairheatmap(mtcars, mtcars[,1:5], scale="rowsep")
pairheatmap(mtcars, mtcars[,1:5], scale="col")
## row group bar
pairheatmap(mtcars, mtcars,
rowGroup=mtcars$gear,
rowNameFontSize=6,
colNameFontSize=6,
rowNameGroupColor=rev(c("blue", "green", "orange")),
rowNameColor="blue",
)
## group options
pairheatmap(mtcars, mtcars,
rowGroup=mtcars$gear,
orderRowGroup=c(5, 4,3)
)
## legend
pairheatmap(mtcars, mtcars,
legend.pos="middle", legend.percent=0.6, legend.fontsize=7)
## cluster analysis
pairheatmap(mtcars, mtcars, clusterMethod="ward", clusterRow=FALSE)
pairheatmap(mtcars, cbind(mtcars, mtcars), clusterColTogether=TRUE)
## selected groups
pairheatmap(mtcars, cbind(mtcars, mtcars),
groupBorder.selectList=
list(xgroup.start=c(2,7), xgroup.end=c(4,9),
ygroup.start=c(3,30), ygroup.end=c(10,32)
))
## more demo
pairheatmap(mtcars, mtcars, legend.percent=1, legend.pos="middle",
groupBorder.selectList=list(xgroup.start=c(2,7), xgroup.end=c(4,9), ygroup.start=c(3,30),
ygroup.end=c(10,32)))
pairheatmap(mtcars, mtcars, scale="row", colorStyle="s3",
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11),
ygroup.start=c(11), ygroup.end=c(15)),
legend.pos="top")
pairheatmap(mtcars, mtcars,
colorStyle="s4", rowGroup=mtcars$gear,
rowGroupColor=TRUE,
rowGroupColor.choice = rev(c("blue", "orange", "green")),
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
legend.pos="top", legend.percent=0.6, legend.fontsize=5, orderRowGroup=c(5, 4,3),
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=TRUE
)
mtcars2 <- mtcars[, rev(1:ncol(mtcars))]
pairheatmap(mtcars, mtcars2,
colorStyle="s1", rowGroup=mtcars$gear,
rowGroupColor=TRUE,
rowGroupColor.choice = rev(c("blue", "orange", "green")),
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
legend.pos="top", legend.percent=0.6, legend.fontsize=5, orderRowGroup=c(5, 4,3),
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=FALSE
)
pairheatmap(mtcars, mtcars,
dendrogram="row", colorStyle="s1", rowGroup=mtcars$am,
rowGroupColor=TRUE,
groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
legend.pos="top", legend.percent=0.6, legend.fontsize=5,
orderRowGroup=c(0,1),
clusterRow=TRUE, clusterCol=TRUE, clusterColTogether=FALSE
)
|
Example output
Loading required package: grid
$rowInd
[1] 31 17 15 16 29 7 24 5 25 4 6 14 12 13 22 23 19 20 18 26 30 28 9 32 3
[26] 21 27 8 1 2 10 11
$colInd1
[1] 1 7 2 8 9 5 10 6 11 3 4
$colInd2
[1] 1 7 2 8 9 5 10 6 11 3 4
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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