Hi Petr; Thanks for your reply. It is much appreciated. A small example is given below for 4 independent and 4 dependent variables only. The values given are regression coefficients.I have looked ggplot documents before writing to you. Unfortunately, I could not figure out as my experience in ggplot is ignorable Regards. Greg y1 y2 y3 y4 x1 -0.19 0.40 -0.06 0.13 x2 0.45 -0.75 -8.67 -0.46 x3 -0.09 0.14 1.42 0.06 x4 -0.16 -0.01 2.21 0.06 On Thu, Feb 8, 2018 at 10:19 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:> Hi > > Example, example, example - preferably working. > > Wild guess - did you try ggplot? > > Cheers > Petr > > > > -----Original Message----- > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg > holly > > Sent: Thursday, February 8, 2018 8:14 AM > > To: r-help mailing list <r-help at r-project.org> > > Subject: [R] plotting the regression coefficients > > > > Hi Dear all; > > > > I would like to create a plot for regression coefficients with each > independent > > variable (x) along the side and the phenotypes (y) across the top (as > given > > below). For each data point, direction and magnitude of effect could be > color > > and significance could be the size of the circle? Is this possible? > > > > > > I would greatly be appreciated your help. > > > > Thanks, > > > > Greg > > > > > > > > y1 y2 y3 y4 y5 y6 > > x1 > > x2 > > x3 > > x4 > > x5 > > x6 > > x7 > > x8 > > x9 > > x10 > > x11 > > x12 > > x13 > > x14 > > x15 > > x16 > > x17 > > . > > . > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ________________________________ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie > vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi > ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany > p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. >[[alternative HTML version deleted]]
Hi I copied your values to R, here it is> dput(temp)temp <- structure(list(par1 = structure(1:4, .Label = c("x1", "x2", "x3", "x4"), class = "factor"), y1 = c(-0.19, 0.45, -0.09, -0.16), y2 = c(0.4, -0.75, 0.14, -0.01), y3 = c(-0.06, -8.67, 1.42, 2.21), y4 = c(0.13, -0.46, 0.06, 0.06)), .Names = c("par1", "y1", "y2", "y3", "y4"), class = "data.frame", row.names = c(NA, -4L)) For plotting it need to be reshaped library(reshape2) library(ggplot2) temp <- melt(temp) p <- ggplot(temp, aes(x=par1, y=variable, size=abs(value), colour=factor(sign(value)))) p+geom_point() Is this what you wanted? Cheers Petr And preferably do not post in HTML, the email content could be scrambled. From: greg holly [mailto:mak.hholly at gmail.com] Sent: Thursday, February 8, 2018 9:23 AM To: PIKAL Petr <petr.pikal at precheza.cz> Cc: r-help mailing list <r-help at r-project.org> Subject: Re: [R] plotting the regression coefficients Hi Petr; Thanks for your reply. It is much appreciated. A small example is given below for 4 independent and 4 dependent variables only. The values given are regression coefficients.I have looked ggplot documents before writing to you. Unfortunately, I could not figure out as my experience in ggplot is ignorable Regards. Greg y1 y2 y3 y4 x1 -0.19 0.40 -0.06 0.13 x2 0.45 -0.75 -8.67 -0.46 x3 -0.09 0.14 1.42 0.06 x4 -0.16 -0.01 2.21 0.06 On Thu, Feb 8, 2018 at 10:19 AM, PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> wrote: Hi Example, example, example - preferably working. Wild guess - did you try ggplot? Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org<mailto:r-help-bounces at r-project.org>] On Behalf Of greg holly > Sent: Thursday, February 8, 2018 8:14 AM > To: r-help mailing list <r-help at r-project.org<mailto:r-help at r-project.org>> > Subject: [R] plotting the regression coefficients > > Hi Dear all; > > I would like to create a plot for regression coefficients with each independent > variable (x) along the side and the phenotypes (y) across the top (as given > below). For each data point, direction and magnitude of effect could be color > and significance could be the size of the circle? Is this possible? > > > I would greatly be appreciated your help. > > Thanks, > > Greg > > > > y1 y2 y3 y4 y5 y6 > x1 > x2 > x3 > x4 > x5 > x6 > x7 > x8 > x9 > x10 > x11 > x12 > x13 > x14 > x15 > x16 > x17 > . > . > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. ________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. [[alternative HTML version deleted]]
Hi Petr; Thanks so much. Exactly this is what I need. I will play to change color and so on but this backbound is perfect to me. I do appreciate your help and support. Regards, Greg On Thu, Feb 8, 2018 at 1:29 PM, PIKAL Petr <petr.pikal at precheza.cz> wrote:> Hi > > I copied your values to R, here it is > > > > > dput(temp) > > > > temp <- structure(list(par1 = structure(1:4, .Label = c("x1", "x2", "x3", > > "x4"), class = "factor"), y1 = c(-0.19, 0.45, -0.09, -0.16), > > y2 = c(0.4, -0.75, 0.14, -0.01), y3 = c(-0.06, -8.67, 1.42, > > 2.21), y4 = c(0.13, -0.46, 0.06, 0.06)), .Names = c("par1", > > "y1", "y2", "y3", "y4"), class = "data.frame", row.names = c(NA, > > -4L)) > > > > For plotting it need to be reshaped > > > > library(reshape2) > > library(ggplot2) > > > > temp <- melt(temp) > > p <- ggplot(temp, aes(x=par1, y=variable, size=abs(value), > colour=factor(sign(value)))) > > p+geom_point() > > > > Is this what you wanted? > > > > Cheers > > Petr > > And preferably do not post in HTML, the email content could be scrambled. > > > > *From:* greg holly [mailto:mak.hholly at gmail.com] > *Sent:* Thursday, February 8, 2018 9:23 AM > *To:* PIKAL Petr <petr.pikal at precheza.cz> > *Cc:* r-help mailing list <r-help at r-project.org> > *Subject:* Re: [R] plotting the regression coefficients > > > > Hi Petr; > > > > Thanks for your reply. It is much appreciated. A small example is given > below for 4 independent and 4 dependent variables only. The values given > are regression coefficients.I have looked ggplot documents before writing > to you. Unfortunately, I could not figure out as my experience in ggplot is > ignorable > > > > Regards. > > Greg > > > > y1 y2 y3 y4 > > x1 -0.19 0.40 -0.06 0.13 > > x2 0.45 -0.75 -8.67 -0.46 > > x3 -0.09 0.14 1.42 0.06 > > x4 -0.16 -0.01 2.21 0.06 > > > > > > On Thu, Feb 8, 2018 at 10:19 AM, PIKAL Petr <petr.pikal at precheza.cz> > wrote: > > Hi > > Example, example, example - preferably working. > > Wild guess - did you try ggplot? > > Cheers > Petr > > > > > -----Original Message----- > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg > holly > > Sent: Thursday, February 8, 2018 8:14 AM > > To: r-help mailing list <r-help at r-project.org> > > Subject: [R] plotting the regression coefficients > > > > Hi Dear all; > > > > I would like to create a plot for regression coefficients with each > independent > > variable (x) along the side and the phenotypes (y) across the top (as > given > > below). For each data point, direction and magnitude of effect could be > color > > and significance could be the size of the circle? Is this possible? > > > > > > I would greatly be appreciated your help. > > > > Thanks, > > > > Greg > > > > > > > > y1 y2 y3 y4 y5 y6 > > x1 > > x2 > > x3 > > x4 > > x5 > > x6 > > x7 > > x8 > > x9 > > x10 > > x11 > > x12 > > x13 > > x14 > > x15 > > x16 > > x17 > > . > > . > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ________________________________ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie > vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi > ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany > p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. > > > > ------------------------------ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie > vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi > ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany > p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > This e-mail and any documents attached to it may be confidential and are > intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a > contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) excludes > any acceptance of the offer on the part of the recipient containing any > amendment or variation. > - the sender insists on that the respective contract is concluded only > upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter > into any contracts on behalf of the company except for cases in which > he/she is expressly authorized to do so in writing, and such authorization > or power of attorney is submitted to the recipient or the person > represented by the recipient, or the existence of such authorization is > known to the recipient of the person represented by the recipient. >[[alternative HTML version deleted]]