circos.JCR: Circular visualization of Journal Citing/Cited Relationships

In PhDMeiwp/circos.JCR: Circular visualization of Journal Citing/Cited Relationships

Description

circos.JCR is a extension of 'circlize' package for drawing the graph of Journal Citing/Cited Relationships. Graph example as http://ipscience-help.thomsonreuters.com/incitesLiveJCR/JCRGroup/jcrJournalProfile/jcrJournalProfileEgoNetwork.html

circos.JCR is a extension of 'circlize' package for drawing the graph of Journal Citing/Cited Relationships. Graph example as http://ipscience-help.thomsonreuters.com/incitesLiveJCR/JCRGroup/jcrJournalProfile/jcrJournalProfileEgoNetwork.html

Usage

circos.JCR(x.cite, JCR.name, x.allcite, col = NULL, transparency = 0.8,
  order.by = 0, text.size = 0.7, self.include = FALSE,
  start.degree = 90, draw.line = FALSE, ...)

circos.JCR(x.cite, JCR.name, x.allcite, col = NULL, transparency = 0.8,
  order.by = 0, text.size = 0.7, self.include = FALSE,
  start.degree = 90, draw.line = FALSE, ...)

Arguments

JCR.name	Journal names (N.B., can NOT rename, i.e. No name is repeated each other).
col	The color for sector.index and circos.link.
transparency	Transparency of color.
order.by	The direction of the circos, 0 = orde by the number of 'x', 1 = order by alphabet for 'JCR.name'.
text.size	The font size of text. Value as cex (e.g., 0.8).
self.include	Whether the link include the parent journal. Default is FALSE.
start.degree	For the start degree of the 1st sector.index. see circos.par.
...	additional parameters to circos.link,such as directional, rou, rou1, tou2, lty, arr.lty.
x	Citing or cited data of JCR in sector.index1. The 1st value in dataset 'x' is the sector.index1 as default.
track.height	The height of one track.index.
x	Citing or cited data of JCR in sector.index1. The 1st value in dataset 'x' is the sector.index1 as default.
JCR.name	Journal names (N.B., can NOT rename, i.e. No name is repeated each other).
col	The color for sector.index and circos.link.
transparency	Transparency of color.
order.by	The direction of the circos, 0 = orde by the number of 'x', 1 = order by alphabet for 'JCR.name'.
self.include	Whether the link include the parent journal. Default is FALSE.
start.degree	For the start degree of the 1st sector.index. see circos.par.
text.size	The font size of text. Value as cex (e.g., 0.8).
track.height	The height of one track.index.
...	additional parameters to circos.link,such as directional, rou, rou1, tou2, lty, arr.lty.

Author(s)

Weiping Mei <[e-mail]>

Weiping Mei <[e-mail]>

See Also

circos.link

circos.link

Examples

library(circos.JCR)
# an example of citing data of journal "Nature", the top 20 cited journals data included.
NatureCiting = c(4665, 2719, 1757, 1279, 713, 630, 556, 445, 441, 413,
                 402,  387,  367,  359,  351, 337, 323, 316, 314, 312, 292)
# Top 20 cited journals by the parent journal "Nature"
JCR.name =c("Nature", "SCIENCE", "P NATL ACAD SCI USA", "CELL", "PHYS REV LETT",
            "ASTROPHYS J", "J BIOL CHEM", "NAT COMMUN", "NUCLEIC ACIDS RES", "PLOS ONE",
             "NEURON", "J AM CHEM SOC", "J NEUROSCI", "BIOINFORMATICS", "MON NOT R ASTRON.",
             "ACTA CRYSTALLOGR D", "NAT METHODS", "MOL CELL", "NAT GENET", "ASTRON ASTROPHYS", "NAT NEUROSCI")
# "Citing data (not exact data)" by the top 20 journals.
Allciting = c(7156,  6564,  12214, 2818, 968,
              19399, 7772, 10489, 6570, 27664,
              2251,  3487, 6329,  1475, 28571,
              501, 600, 1198, 668, 10747, 2460)

circos.JCR(x.cite = NatureCiting, JCR.name = JCR.name, x.allcite = Allciting, start.degree = 90, order.by = 0, text.size = 0.7)


library(circos.JCR)
NatureCiting = c(4665, 2719, 1757, 1279, 713, 630, 556, 445, 441, 413,
                 402,  387,  367,  359,  351)
JCR.name =c("Nature", "SCIENCE", "P NATL ACAD SCI USA", "CELL", "PHYS REV LETT",
            "ASTROPHYS J", "J BIOL CHEM", "NAT COMMUN", "NUCLEIC ACIDS RES", "PLOS ONE",
             "NEURON", "J AM CHEM SOC", "J NEUROSCI", "BIOINFORMATICS", "MON NOT R ASTRON.")
Allciting = c(7156,  6564,  12214, 2818, 968,
              19399, 7772, 10489, 6570, 27664,
              2251,  3487, 6329,  1475, 28571)

circos.JCR(x.cite = NatureCiting, JCR.name = JCR.name, x.allcite = Allciting, start.degree = 90, order.by = 0, text.size = 0.7)

PhDMeiwp/circos.JCR documentation built on May 30, 2019, 11:41 a.m.