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Old 04-07-2013, 05:40 PM   #1
Seq_student
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Location: California

Join Date: Jun 2012
Posts: 5
Default CummeRbund: csHeatmap - How to extract the ordered list of gene Ids?

Hello all,

I was wondering if someone could direct me to where the ordered list of geneIDs for the ggplot object (heatmap) produced by csHeatmap() is located? I'm a newbie to R and I can't find the variable storing the list of geneIDs. I made a heatmap of ~600 sig. genes but the text labels for the gene IDs are all mashed together and unreadable. I'd like to extract this ordered list (the rows of genes have been clustered) and make a new axis label myself in another program (can't find a way to do it in R).

Does anyone have any ideas? When I use head(object) I see this:
> head(h)
$data
rowInd colInd variable value
1 1 1 norm 1.088128998
2 2 1 norm 0.936610242
....


$layers
$layers[[1]]
mapping: xmin = colInd - 1, xmax = colInd, ymin = rowInd - 1, ymax = rowInd, fill = value
geom_rect:
stat_identity:
position_identity: (width = NULL, height = NULL)


$scales
Reference class object of class "Scales"
Field "scales":
[[1]]
continuous_scale(aesthetics = c("x", "xmin", "xmax", "xend",
"xintercept"), scale_name = "position_c", palette = identity,
breaks = ..1, labels = ..2, expand = expand, guide = "none")

[[2]]
continuous_scale(aesthetics = c("y", "ymin", "ymax", "yend",
"yintercept", "ymin_final", "ymax_final"), scale_name = "position_c",
palette = identity, breaks = ..1, labels = ..2, expand = expand,
guide = "none")

[[3]]
continuous_scale(aesthetics = "fill", scale_name = "gradient2",
palette = div_gradient_pal(low, mid, high, space), name = ..1,
rescaler = mid_rescaler(mid = midpoint), na.value = na.value,
guide = guide)


$mapping
list()

$theme
List of 5
$ axis.ticks : list()
..- attr(*, "class")= chr [1:2] "element_blank" "element"
$ panel.grid.minor:List of 4
..$ colour : logi NA
..$ size : num 0.25
..$ linetype: NULL
..$ lineend : NULL
..- attr(*, "class")= chr [1:2] "element_line" "element"
$ panel.grid.major:List of 4
..$ colour : logi NA
..$ size : NULL
..$ linetype: NULL
..$ lineend : NULL
..- attr(*, "class")= chr [1:2] "element_line" "element"
$ panel.background:List of 4
..$ fill : logi NA
..$ colour : logi NA
..$ size : NULL
..$ linetype: NULL
..- attr(*, "class")= chr [1:2] "element_rect" "element"
$ axis.text.x :List of 8
..$ family : NULL
..$ face : NULL
..$ colour : NULL
..$ size : NULL
..$ hjust : num 0
..$ vjust : num 1
..$ angle : num -90
..$ lineheight: NULL
..- attr(*, "class")= chr [1:2] "element_text" "element"
- attr(*, "class")= chr [1:2] "theme" "gg"
- attr(*, "complete")= logi FALSE

$coordinates
$limits
$limits$x
NULL

$limits$y
NULL


attr(,"class")
[1] "cartesian" "coord


The gene ids are not stored in h$data. Is anyone familiar enough with ggplot objects that they can lend me a hand?

Many thanks!
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