keggColor: Color Pathway

In VonWebEinstein/keggAPI: KEGG API

Description

Color Pathway is an advanced version of the KEGG pathway mapping tool, where given objects (genes, proteins, compounds, glycans, reactions, drugs, etc.) are searched against KEGG pathway maps and found objects are marked in any background and foreground colors (bgcolor and fgcolor).

Usage

keggColor(map, mapping_list = NULL, mode = "color", log = 0,
          numericalType = "mm", minColor = "#ffff00", maxColor = "#ff0000",
          negativeColor = "#00ff00", zeroColor = "#ffff00", positiveColor = "#ff0000")

keggColor(map, filename = NULL, mode = "color", log = 0,
          numericalType = "mm", minColor = "#ffff00", maxColor = "#ff0000",
          negativeColor = "#00ff00", zeroColor = "#ffff00", positiveColor = "#ff0000")

Arguments

map	string. Pathway ID.
mapping_list	string. The coded entries and colors/numbers.
filename	string. File that contains entries and colors/numbers, same effect as mapping_list.
mode	"color" or "number". Use "Color specification" or "Numerical value".
log	1 or 0. Convert to log scale or not.
numericalType	"mm" or "nzp". Gradation with minimum-maximum or negative-zero-positive.
minColor, maxColor	Give the colors at minimum and maixmum.
negativeColor, zeroColor, positiveColor	Give the colors at negative, zero and positive.
path	string. Path to save images.

Details

For each entry, the format is /keggid%09bgcolor,fgcolor or /keggid%09number in mapping_list, the format is keggid bgcolor,fgcolor or keggid number in each line in the file.

When mode = "number" and numericalType = "mm"(Gradation with minimum-maximum), we just need minColor and maxColor. When mode = "number" and numericalType = "nzp"(Gradation with negative-zero-positive), we just need negativeColor, zeroColor and positiveColor. When mode = "color", we need none of them.

Examples

# "%09" represents TAB in ASCII code
# Use "%23" in ASCII code instead of "#" for color specification.
# color mode
keggColor(map = "map00400",
          mapping_list = "/1.14.16.1%09,blue/C00079%09,red/C00166%09%23005050")

# numer mode
keggColor(map = "map00400",
          mapping_list = "/1.14.16.1%091/C00079%092/C00166%093",
          mode = "number")

# give filename, color mode
#save txt
download.file(url = "http://www.kegg.jp/kegg/tool/example/hsa_CML.txt",
              destfile = "hsa_CML.txt",
              mode ="wb")
keggColor(map = "hsa05200",
          filename = "hsa_CML.txt")

# give filename, number mode
download.file(url = "http://www.kegg.jp/kegg/tool/example/hsa_CML-COSMIC.txt",
              destfile = "hsa_CML-COSMIC.txt",
              mode ="wb")
keggColor(map = "hsa05200",
          filename = "hsa_CML-COSMIC.txt",
          mode = "number")

VonWebEinstein/keggAPI documentation built on May 9, 2019, 10:02 p.m.