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annotate histogram.r @ 0:a87a3773d8ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
author iuc
date Fri, 09 Mar 2018 08:23:08 -0500
parents
children 344ac3ca7557
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
parents:
diff changeset
1 # wrapper
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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2 wrapper <- function(table, columns, options) {
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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3
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
parents:
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4 # initialize output list
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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5 l <- list()
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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6
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
parents:
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7 # loop through all columns
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
parents:
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8 m <- list()
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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9 for (key in names(columns)) {
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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10 # load column data
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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11 column <- as.numeric(columns[key])
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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12 column_data <- suppressWarnings(as.numeric(as.character(table[column][[1]])))
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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13
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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14 # collect vectors in list
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
parents:
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15 m <- append(m, list(column_data))
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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16 }
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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18 # identify optimal breaks
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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19 hist_data <- hist(unlist(m), plot=FALSE)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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20 breaks <- hist_data$breaks;
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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22 # add as first column
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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23 l <- append(l, list(breaks[2: length(breaks)]))
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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24
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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25 # loop through all columns
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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26 for (key in seq(m)) {
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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27 # load column data
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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28 column_data <- m[[key]]
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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29
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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30 # create hist data
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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31 hist_data <- hist(column_data, breaks=breaks, plot=FALSE)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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32
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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33 # normalize densities
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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34 count_sum <- sum(hist_data$counts)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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35 if (count_sum > 0) {
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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36 hist_data$counts = hist_data$counts / count_sum
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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37 }
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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39 # collect vectors in list
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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40 l <- append(l, list(hist_data$counts))
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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41 }
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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43 # return
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
iuc
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44 return (l)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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45 }